Starting phenix.real_space_refine on Fri Aug 7 08:53:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umt_42383/08_2026/8umt_42383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umt_42383/08_2026/8umt_42383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8umt_42383/08_2026/8umt_42383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umt_42383/08_2026/8umt_42383.map" model { file = "/net/cci-nas-00/data/ceres_data/8umt_42383/08_2026/8umt_42383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umt_42383/08_2026/8umt_42383.cif" } resolution = 3.33 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= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 3 5.21 5 S 135 5.16 5 C 13022 2.51 5 N 3568 2.21 5 O 3958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20697 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4255 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 504} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2492 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2563 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "D" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2512 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "E" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2745 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 15, 'TRANS': 329} Chain: "F" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1989 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.36, per 1000 atoms: 0.21 Number of scatterers: 20697 At special positions: 0 Unit cell: (115.92, 120.888, 147.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 135 16.00 P 11 15.00 Mg 3 11.99 O 3958 8.00 N 3568 7.00 C 13022 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: 1.70 Conformation dependent library (CDL) restraints added in 1.0 seconds 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4994 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 15 sheets defined 50.4% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 311 through 314 Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.542A pdb=" N ALA A 505 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 530 removed outlier: 3.780A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 549 through 563 Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.584A pdb=" N VAL A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 595 removed outlier: 3.571A pdb=" N GLN A 591 " --> pdb=" O PHE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 645 through 656 Processing helix chain 'A' and resid 668 through 690 Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.734A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 704 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 744 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.697A pdb=" N SER A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'A' and resid 782 through 800 Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.971A pdb=" N LEU A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 863 Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.628A pdb=" N TYR B 42 " --> pdb=" O TRP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 54 through 67 removed outlier: 3.687A pdb=" N ARG B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.889A pdb=" N VAL B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.204A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.743A pdb=" N ARG B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 256 removed outlier: 4.029A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.968A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.759A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 37 through 50 removed outlier: 3.580A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.624A pdb=" N ILE C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 127 through 130 removed outlier: 3.607A pdb=" N MET C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 127 through 130' Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.666A pdb=" N LYS C 160 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 178 through 193 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 209 Processing helix chain 'C' and resid 212 through 227 removed outlier: 3.527A pdb=" N ALA C 216 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 256 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 294 through 314 Processing helix chain 'C' and resid 317 through 340 removed outlier: 4.024A pdb=" N GLN C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 55 through 69 removed outlier: 3.701A pdb=" N ALA D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 104 Proline residue: D 98 - end of helix removed outlier: 4.345A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 128 removed outlier: 3.947A pdb=" N VAL D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 removed outlier: 3.627A pdb=" N MET D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 152 through 155' Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.603A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.663A pdb=" N ARG D 193 " --> pdb=" O PRO D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 234 Processing helix chain 'D' and resid 237 through 253 Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.788A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 removed outlier: 3.577A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 320 through 341 Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.624A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.850A pdb=" N GLU E 65 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 100 removed outlier: 3.847A pdb=" N ASP E 99 " --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA E 100 " --> pdb=" O PRO E 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 100' Processing helix chain 'E' and resid 103 through 117 removed outlier: 3.837A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 removed outlier: 3.654A pdb=" N CYS E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.948A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 Processing helix chain 'E' and resid 287 through 301 Processing helix chain 'E' and resid 306 through 323 removed outlier: 4.165A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.248A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.859A pdb=" N ILE F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.838A pdb=" N SER F 222 " --> pdb=" O THR F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 20 removed outlier: 4.510A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing helix chain 'H' and resid 8 through 10 No H-bonds generated for 'chain 'H' and resid 8 through 10' Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 79 removed outlier: 3.568A pdb=" N LYS H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 190 through 194 removed outlier: 4.012A pdb=" N GLU H 193 " --> pdb=" O LYS H 190 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA H 194 " --> pdb=" O GLU H 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 190 through 194' Processing helix chain 'H' and resid 209 through 217 Processing helix chain 'H' and resid 218 through 222 removed outlier: 3.857A pdb=" N LEU H 221 " --> pdb=" O ALA H 218 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER H 222 " --> pdb=" O THR H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 218 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 399 removed outlier: 5.888A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET A 398 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 532 through 533 removed outlier: 7.933A pdb=" N ARG A 532 " --> pdb=" O LEU A 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 803 through 807 Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.227A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.566A pdb=" N LEU C 88 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASP C 125 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 90 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 122 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.183A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 75 through 77 removed outlier: 5.673A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASP D 150 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU D 108 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.192A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 59 through 62 removed outlier: 4.212A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN G 177 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 7.260A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 204 through 208 removed outlier: 5.483A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL F 167 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR H 59 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.860A pdb=" N VAL G 111 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS H 181 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.969A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 71 removed outlier: 3.592A pdb=" N LEU H 66 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) 1103 hydrogen bonds defined for protein. 3177 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: 4.78 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6966 1.36 - 1.51: 5077 1.51 - 1.65: 8779 1.65 - 1.80: 120 1.80 - 1.95: 85 Bond restraints: 21027 Sorted by residual: bond pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O3B AGS B 402 " pdb=" PB AGS B 402 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CA LYS H 217 " pdb=" C LYS H 217 " ideal model delta sigma weight residual 1.522 1.583 -0.061 1.43e-02 4.89e+03 1.83e+01 bond pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " ideal model delta sigma weight residual 1.664 1.580 0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 21022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 27818 2.24 - 4.47: 522 4.47 - 6.71: 67 6.71 - 8.94: 40 8.94 - 11.18: 7 Bond angle restraints: 28454 Sorted by residual: angle pdb=" N TYR E 343 " pdb=" CA TYR E 343 " pdb=" C TYR E 343 " ideal model delta sigma weight residual 111.14 106.05 5.09 1.08e+00 8.57e-01 2.22e+01 angle pdb=" N ASP F 156 " pdb=" CA ASP F 156 " pdb=" C ASP F 156 " ideal model delta sigma weight residual 114.31 108.23 6.08 1.29e+00 6.01e-01 2.22e+01 angle pdb=" C THR A 417 " pdb=" N GLN A 418 " pdb=" CA GLN A 418 " ideal model delta sigma weight residual 122.61 129.22 -6.61 1.56e+00 4.11e-01 1.80e+01 angle pdb=" C GLY E 33 " pdb=" N ASP E 34 " pdb=" CA ASP E 34 " ideal model delta sigma weight residual 122.82 128.83 -6.01 1.42e+00 4.96e-01 1.79e+01 angle pdb=" N GLU D 188 " pdb=" CA GLU D 188 " pdb=" C GLU D 188 " ideal model delta sigma weight residual 113.25 118.71 -5.46 1.30e+00 5.92e-01 1.76e+01 ... (remaining 28449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.19: 12703 34.19 - 68.37: 314 68.37 - 102.56: 28 102.56 - 136.75: 2 136.75 - 170.93: 4 Dihedral angle restraints: 13051 sinusoidal: 5377 harmonic: 7674 Sorted by residual: dihedral pdb=" C5' ADP E2000 " pdb=" O5' ADP E2000 " pdb=" PA ADP E2000 " pdb=" O2A ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 169.07 130.93 1 2.00e+01 2.50e-03 3.97e+01 dihedral pdb=" O1B ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PB ADP E2000 " pdb=" PA ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 -163.80 103.80 1 2.00e+01 2.50e-03 2.97e+01 dihedral pdb=" O1A AGS B 402 " pdb=" O3A AGS B 402 " pdb=" PA AGS B 402 " pdb=" PB AGS B 402 " ideal model delta sinusoidal sigma weight residual 82.37 -106.70 -170.93 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2686 0.058 - 0.117: 529 0.117 - 0.175: 88 0.175 - 0.234: 3 0.234 - 0.292: 5 Chirality restraints: 3311 Sorted by residual: chirality pdb=" C3' AGS D 402 " pdb=" C2' AGS D 402 " pdb=" C4' AGS D 402 " pdb=" O3' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C3' AGS B 402 " pdb=" C2' AGS B 402 " pdb=" C4' AGS B 402 " pdb=" O3' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' AGS C 402 " pdb=" C2' AGS C 402 " pdb=" C4' AGS C 402 " pdb=" O3' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3308 not shown) Planarity restraints: 3643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " -0.065 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO A 699 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 293 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C GLU A 293 " 0.065 2.00e-02 2.50e+03 pdb=" O GLU A 293 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 294 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 76 " 0.051 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO E 77 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 77 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 77 " 0.043 5.00e-02 4.00e+02 ... (remaining 3640 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 214 2.62 - 3.19: 16863 3.19 - 3.76: 32679 3.76 - 4.33: 43253 4.33 - 4.90: 71982 Nonbonded interactions: 164991 Sorted by model distance: nonbonded pdb="MG MG B 401 " pdb=" O1B AGS B 402 " model vdw 2.048 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2G AGS B 402 " model vdw 2.071 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.080 2.170 nonbonded pdb="MG MG D 401 " pdb=" O3G AGS D 402 " model vdw 2.082 2.170 nonbonded pdb="MG MG B 401 " pdb=" O1A AGS B 402 " model vdw 2.107 2.170 ... (remaining 164986 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 'G' and resid 1 through 258) selection = (chain 'H' and resid 1 through 258) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.560 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 21027 Z= 0.235 Angle : 0.799 11.181 28454 Z= 0.434 Chirality : 0.049 0.292 3311 Planarity : 0.007 0.098 3643 Dihedral : 15.241 170.931 8057 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 4.14 % Allowed : 11.52 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.15), residues: 2601 helix: -1.46 (0.12), residues: 1208 sheet: -0.65 (0.23), residues: 513 loop : -1.46 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 311 TYR 0.012 0.001 TYR D 77 PHE 0.015 0.002 PHE F 169 TRP 0.009 0.001 TRP H 28 HIS 0.005 0.001 HIS C 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.24 (21027) covalent geometry : angle 0.79910 / 0.43 (28454) hydrogen bonds : bond 0.13946 / 9.85 ( 1103) hydrogen bonds : angle 6.43190 / 4.52 ( 3177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 473 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 MET cc_start: 0.5988 (tpp) cc_final: 0.5635 (tpp) REVERT: A 843 LEU cc_start: 0.8676 (tp) cc_final: 0.8456 (tp) REVERT: B 38 TRP cc_start: 0.7185 (m-10) cc_final: 0.6967 (m-10) REVERT: B 245 PHE cc_start: 0.7011 (t80) cc_final: 0.6804 (t80) REVERT: D 238 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8210 (tt) REVERT: E 155 TYR cc_start: 0.5786 (m-80) cc_final: 0.5361 (m-80) REVERT: F 1 MET cc_start: 0.4277 (ppp) cc_final: 0.3350 (ppp) REVERT: F 14 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8115 (ttpp) REVERT: G 87 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6516 (pp) REVERT: G 143 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: G 154 ILE cc_start: 0.5604 (OUTLIER) cc_final: 0.5277 (tp) outliers start: 95 outliers final: 19 residues processed: 545 average time/residue: 0.1693 time to fit residues: 139.0193 Evaluate side-chains 337 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 314 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.0970 chunk 258 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 655 ASN A 690 GLN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN E 194 HIS E 213 HIS ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN G 36 ASN G 65 ASN G 246 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.189691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.154520 restraints weight = 34219.945| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.83 r_work: 0.3967 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21027 Z= 0.194 Angle : 0.672 10.984 28454 Z= 0.342 Chirality : 0.044 0.166 3311 Planarity : 0.006 0.082 3643 Dihedral : 10.283 159.643 2991 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.66 % Allowed : 15.97 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2601 helix: -0.23 (0.14), residues: 1225 sheet: -0.52 (0.23), residues: 516 loop : -1.08 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 149 TYR 0.020 0.002 TYR E 254 PHE 0.023 0.002 PHE H 207 TRP 0.012 0.002 TRP H 28 HIS 0.014 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (21027) covalent geometry : angle 0.67209 / 0.34 (28454) hydrogen bonds : bond 0.04193 / 2.79 ( 1103) hydrogen bonds : angle 4.98125 / 3.53 ( 3177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 350 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 LEU cc_start: 0.9258 (tp) cc_final: 0.9013 (tp) REVERT: F 1 MET cc_start: 0.6145 (ppp) cc_final: 0.4883 (ppp) REVERT: F 14 LYS cc_start: 0.9251 (mmtt) cc_final: 0.8702 (mtpp) REVERT: F 60 TYR cc_start: 0.3872 (t80) cc_final: 0.3582 (t80) REVERT: F 99 LEU cc_start: 0.8306 (pp) cc_final: 0.7986 (tp) REVERT: F 144 PHE cc_start: 0.8819 (t80) cc_final: 0.8419 (t80) REVERT: F 148 CYS cc_start: 0.8964 (m) cc_final: 0.8651 (m) REVERT: G 13 LYS cc_start: 0.8318 (ttmm) cc_final: 0.7775 (mttp) REVERT: G 87 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7096 (pp) outliers start: 84 outliers final: 50 residues processed: 404 average time/residue: 0.1691 time to fit residues: 102.8384 Evaluate side-chains 347 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 296 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 235 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 238 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 240 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS E 244 GLN F 184 GLN H 44 HIS H 131 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.184183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.139930 restraints weight = 34121.705| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.18 r_work: 0.3748 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21027 Z= 0.174 Angle : 0.639 11.743 28454 Z= 0.324 Chirality : 0.043 0.217 3311 Planarity : 0.005 0.078 3643 Dihedral : 9.662 160.498 2968 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.84 % Allowed : 17.32 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2601 helix: 0.21 (0.15), residues: 1237 sheet: -0.53 (0.23), residues: 514 loop : -0.94 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 93 TYR 0.015 0.002 TYR B 279 PHE 0.018 0.002 PHE E 339 TRP 0.028 0.002 TRP A 307 HIS 0.013 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (21027) covalent geometry : angle 0.63947 / 0.32 (28454) hydrogen bonds : bond 0.03844 / 2.54 ( 1103) hydrogen bonds : angle 4.80407 / 3.40 ( 3177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 336 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6441 (pm20) REVERT: A 843 LEU cc_start: 0.9358 (tp) cc_final: 0.9137 (tp) REVERT: B 199 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8007 (mm) REVERT: B 210 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7728 (ttp80) REVERT: E 119 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.5967 (pm20) REVERT: E 150 ARG cc_start: 0.8650 (ttp-110) cc_final: 0.8136 (ttp-110) REVERT: F 1 MET cc_start: 0.6505 (ppp) cc_final: 0.5311 (ppp) REVERT: F 14 LYS cc_start: 0.9207 (mmtt) cc_final: 0.8569 (mtpp) REVERT: F 40 MET cc_start: 0.6383 (tpp) cc_final: 0.6132 (tpt) REVERT: F 60 TYR cc_start: 0.4221 (t80) cc_final: 0.3938 (t80) REVERT: F 99 LEU cc_start: 0.8477 (pp) cc_final: 0.8236 (tp) REVERT: F 112 SER cc_start: 0.8344 (m) cc_final: 0.7268 (p) REVERT: F 144 PHE cc_start: 0.8859 (t80) cc_final: 0.8494 (t80) REVERT: F 148 CYS cc_start: 0.9048 (m) cc_final: 0.8732 (m) REVERT: G 13 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7681 (mttp) REVERT: G 87 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7028 (pp) REVERT: H 116 MET cc_start: 0.7395 (ttm) cc_final: 0.6971 (ttt) outliers start: 88 outliers final: 54 residues processed: 394 average time/residue: 0.1627 time to fit residues: 97.6383 Evaluate side-chains 363 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 305 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 155 TYR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 147 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 29 optimal weight: 0.0870 chunk 13 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 106 optimal weight: 0.0270 chunk 213 optimal weight: 3.9990 overall best weight: 1.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 ASN A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 301 HIS E 92 HIS E 194 HIS E 213 HIS G 8 GLN H 131 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.191567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.157228 restraints weight = 34157.626| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 2.64 r_work: 0.4006 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21027 Z= 0.133 Angle : 0.613 10.527 28454 Z= 0.308 Chirality : 0.042 0.221 3311 Planarity : 0.005 0.075 3643 Dihedral : 9.294 159.878 2962 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.93 % Allowed : 17.98 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2601 helix: 0.50 (0.15), residues: 1238 sheet: -0.51 (0.22), residues: 523 loop : -0.87 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 150 TYR 0.020 0.001 TYR B 213 PHE 0.040 0.002 PHE F 215 TRP 0.020 0.001 TRP A 307 HIS 0.010 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (21027) covalent geometry : angle 0.61287 / 0.31 (28454) hydrogen bonds : bond 0.03505 / 2.32 ( 1103) hydrogen bonds : angle 4.64675 / 3.29 ( 3177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 339 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: A 843 LEU cc_start: 0.9323 (tp) cc_final: 0.9114 (tp) REVERT: E 105 ARG cc_start: 0.7799 (ptp-170) cc_final: 0.7221 (ptp-170) REVERT: E 119 GLN cc_start: 0.6702 (OUTLIER) cc_final: 0.5900 (pm20) REVERT: E 150 ARG cc_start: 0.8594 (ttp-110) cc_final: 0.8085 (ttp-110) REVERT: F 1 MET cc_start: 0.6254 (ppp) cc_final: 0.5120 (ppp) REVERT: F 14 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8751 (mtpp) REVERT: F 40 MET cc_start: 0.6453 (tpp) cc_final: 0.6203 (tpt) REVERT: F 53 ARG cc_start: 0.8872 (ptp-110) cc_final: 0.8322 (mtm110) REVERT: F 60 TYR cc_start: 0.3875 (t80) cc_final: 0.3475 (t80) REVERT: F 112 SER cc_start: 0.8386 (m) cc_final: 0.7391 (p) REVERT: F 148 CYS cc_start: 0.8906 (m) cc_final: 0.8595 (m) REVERT: G 13 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7690 (mttp) REVERT: G 87 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.6909 (pp) REVERT: G 125 GLN cc_start: 0.6902 (tm-30) cc_final: 0.6613 (tm-30) REVERT: G 146 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7614 (ptp90) outliers start: 90 outliers final: 60 residues processed: 399 average time/residue: 0.1567 time to fit residues: 96.1096 Evaluate side-chains 367 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 303 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 146 ARG Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 44 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 229 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 22 GLN E 213 HIS G 177 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.185158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.148936 restraints weight = 34434.839| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.87 r_work: 0.3876 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21027 Z= 0.194 Angle : 0.666 11.332 28454 Z= 0.335 Chirality : 0.044 0.170 3311 Planarity : 0.005 0.074 3643 Dihedral : 9.255 165.990 2960 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.41 % Allowed : 18.41 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.16), residues: 2601 helix: 0.40 (0.15), residues: 1237 sheet: -0.52 (0.23), residues: 522 loop : -0.87 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 210 TYR 0.015 0.002 TYR B 279 PHE 0.030 0.002 PHE E 339 TRP 0.020 0.002 TRP A 307 HIS 0.008 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (21027) covalent geometry : angle 0.66577 / 0.33 (28454) hydrogen bonds : bond 0.03799 / 2.52 ( 1103) hydrogen bonds : angle 4.74666 / 3.35 ( 3177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 333 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6548 (pm20) REVERT: A 409 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: A 853 MET cc_start: 0.9104 (mmm) cc_final: 0.8873 (mmp) REVERT: B 155 ARG cc_start: 0.7342 (mtp85) cc_final: 0.6766 (mtp85) REVERT: B 176 LYS cc_start: 0.7333 (mtmt) cc_final: 0.7128 (mtmm) REVERT: B 229 MET cc_start: 0.7081 (tpp) cc_final: 0.6873 (tpp) REVERT: D 240 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8387 (mtpp) REVERT: D 246 GLN cc_start: 0.6861 (tp40) cc_final: 0.6474 (tp-100) REVERT: E 105 ARG cc_start: 0.7847 (ptp-170) cc_final: 0.7244 (ptp-170) REVERT: E 119 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.5944 (pm20) REVERT: F 1 MET cc_start: 0.6375 (ppp) cc_final: 0.5070 (ppp) REVERT: F 14 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8923 (mmtp) REVERT: F 53 ARG cc_start: 0.8908 (ptp-110) cc_final: 0.8347 (mtm110) REVERT: F 91 ARG cc_start: 0.6524 (ptm-80) cc_final: 0.6154 (ptm-80) REVERT: F 99 LEU cc_start: 0.7884 (tp) cc_final: 0.7651 (pp) REVERT: F 148 CYS cc_start: 0.8905 (m) cc_final: 0.8696 (m) REVERT: G 13 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7733 (mttp) REVERT: G 87 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7040 (pp) REVERT: H 27 CYS cc_start: 0.8239 (t) cc_final: 0.7842 (p) REVERT: H 116 MET cc_start: 0.7260 (ttm) cc_final: 0.7025 (ttt) outliers start: 101 outliers final: 74 residues processed: 402 average time/residue: 0.1583 time to fit residues: 96.6561 Evaluate side-chains 382 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 303 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 189 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 111 optimal weight: 0.1980 chunk 235 optimal weight: 10.0000 chunk 194 optimal weight: 50.0000 chunk 179 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 430 ASN A 523 GLN A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 194 HIS E 213 HIS ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.189834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.154186 restraints weight = 34060.851| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.69 r_work: 0.3989 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21027 Z= 0.131 Angle : 0.625 7.862 28454 Z= 0.313 Chirality : 0.043 0.283 3311 Planarity : 0.005 0.076 3643 Dihedral : 8.983 175.448 2960 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.28 % Allowed : 19.24 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2601 helix: 0.67 (0.15), residues: 1229 sheet: -0.47 (0.23), residues: 518 loop : -0.77 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 210 TYR 0.017 0.001 TYR B 213 PHE 0.036 0.002 PHE E 339 TRP 0.017 0.001 TRP A 307 HIS 0.007 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (21027) covalent geometry : angle 0.62472 / 0.31 (28454) hydrogen bonds : bond 0.03395 / 2.24 ( 1103) hydrogen bonds : angle 4.57813 / 3.23 ( 3177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 336 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8197 (t80) cc_final: 0.7593 (m-80) REVERT: A 853 MET cc_start: 0.9200 (mmm) cc_final: 0.8981 (mmp) REVERT: B 102 MET cc_start: 0.7744 (tpp) cc_final: 0.7081 (tpt) REVERT: B 176 LYS cc_start: 0.7222 (mtmt) cc_final: 0.7012 (mtmm) REVERT: B 210 ARG cc_start: 0.7037 (ttp80) cc_final: 0.6519 (ttp80) REVERT: D 240 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8362 (mtpp) REVERT: D 246 GLN cc_start: 0.6786 (tp40) cc_final: 0.6451 (tp-100) REVERT: E 21 GLU cc_start: 0.8016 (pt0) cc_final: 0.7628 (pm20) REVERT: E 105 ARG cc_start: 0.7722 (ptp-170) cc_final: 0.7150 (ptp-170) REVERT: E 119 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.5906 (pm20) REVERT: F 14 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8908 (mmtp) REVERT: F 53 ARG cc_start: 0.8836 (ptp-110) cc_final: 0.8279 (mtm110) REVERT: F 61 ARG cc_start: 0.8604 (ptp90) cc_final: 0.7929 (ptm-80) REVERT: F 91 ARG cc_start: 0.6561 (ptm-80) cc_final: 0.6003 (ptm-80) REVERT: F 144 PHE cc_start: 0.8717 (t80) cc_final: 0.8416 (t80) REVERT: F 148 CYS cc_start: 0.8904 (m) cc_final: 0.8691 (m) REVERT: G 13 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7695 (mttp) REVERT: G 87 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.6970 (pp) REVERT: G 125 GLN cc_start: 0.6919 (tm-30) cc_final: 0.6682 (tm-30) REVERT: H 27 CYS cc_start: 0.8145 (t) cc_final: 0.7734 (p) REVERT: H 131 GLN cc_start: 0.6754 (tm130) cc_final: 0.6063 (tm-30) outliers start: 98 outliers final: 75 residues processed: 401 average time/residue: 0.1542 time to fit residues: 93.3086 Evaluate side-chains 385 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 307 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 248 optimal weight: 5.9990 chunk 191 optimal weight: 0.0000 chunk 98 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 232 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 overall best weight: 1.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 213 HIS ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.188225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.153192 restraints weight = 34160.736| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.55 r_work: 0.3978 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21027 Z= 0.170 Angle : 0.659 10.394 28454 Z= 0.331 Chirality : 0.044 0.262 3311 Planarity : 0.005 0.075 3643 Dihedral : 9.015 179.332 2960 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.49 % Allowed : 19.55 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2601 helix: 0.57 (0.15), residues: 1230 sheet: -0.50 (0.23), residues: 516 loop : -0.81 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 140 TYR 0.014 0.001 TYR E 318 PHE 0.031 0.002 PHE E 339 TRP 0.020 0.002 TRP A 307 HIS 0.006 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (21027) covalent geometry : angle 0.65884 / 0.33 (28454) hydrogen bonds : bond 0.03632 / 2.39 ( 1103) hydrogen bonds : angle 4.64654 / 3.28 ( 3177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 318 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8245 (t80) cc_final: 0.7632 (m-80) REVERT: A 853 MET cc_start: 0.9240 (mmm) cc_final: 0.9020 (mmp) REVERT: B 102 MET cc_start: 0.7932 (tpp) cc_final: 0.7232 (tpt) REVERT: B 210 ARG cc_start: 0.7033 (ttp80) cc_final: 0.6515 (ttp80) REVERT: B 229 MET cc_start: 0.6997 (tpp) cc_final: 0.6735 (tpp) REVERT: D 240 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8346 (mtpp) REVERT: D 246 GLN cc_start: 0.6858 (tp40) cc_final: 0.6460 (tp-100) REVERT: E 105 ARG cc_start: 0.7735 (ptp-170) cc_final: 0.7170 (ptp-170) REVERT: E 119 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.5926 (pm20) REVERT: F 53 ARG cc_start: 0.8829 (ptp-110) cc_final: 0.8259 (mtm110) REVERT: F 139 MET cc_start: 0.3098 (OUTLIER) cc_final: 0.2606 (ppp) REVERT: F 144 PHE cc_start: 0.8800 (t80) cc_final: 0.8412 (t80) REVERT: F 148 CYS cc_start: 0.8978 (m) cc_final: 0.8771 (m) REVERT: G 13 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7690 (mttp) REVERT: G 87 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.6982 (pp) REVERT: G 125 GLN cc_start: 0.7023 (tm-30) cc_final: 0.6784 (tm-30) REVERT: G 146 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7584 (ptp90) REVERT: H 27 CYS cc_start: 0.8274 (t) cc_final: 0.7873 (p) outliers start: 103 outliers final: 80 residues processed: 392 average time/residue: 0.1658 time to fit residues: 99.3613 Evaluate side-chains 384 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 299 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 146 ARG Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 44 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 194 HIS E 213 HIS F 8 GLN F 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.190197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.154775 restraints weight = 34116.211| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.68 r_work: 0.3998 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21027 Z= 0.126 Angle : 0.640 11.059 28454 Z= 0.321 Chirality : 0.043 0.248 3311 Planarity : 0.005 0.075 3643 Dihedral : 8.860 177.293 2960 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.75 % Allowed : 20.33 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2601 helix: 0.77 (0.15), residues: 1230 sheet: -0.41 (0.23), residues: 500 loop : -0.72 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 51 TYR 0.018 0.001 TYR B 213 PHE 0.033 0.001 PHE E 339 TRP 0.008 0.001 TRP F 28 HIS 0.004 0.001 HIS E 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (21027) covalent geometry : angle 0.64015 / 0.32 (28454) hydrogen bonds : bond 0.03330 / 2.19 ( 1103) hydrogen bonds : angle 4.49823 / 3.18 ( 3177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 329 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 TRP cc_start: 0.7240 (t60) cc_final: 0.6556 (t60) REVERT: A 409 PHE cc_start: 0.8236 (t80) cc_final: 0.7616 (m-80) REVERT: A 853 MET cc_start: 0.9265 (mmm) cc_final: 0.9043 (mmp) REVERT: B 102 MET cc_start: 0.7809 (tpp) cc_final: 0.7116 (tpt) REVERT: B 155 ARG cc_start: 0.7165 (mtp85) cc_final: 0.6728 (mtp85) REVERT: B 193 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7228 (mm) REVERT: B 210 ARG cc_start: 0.6975 (ttp80) cc_final: 0.6518 (ttp80) REVERT: B 229 MET cc_start: 0.6952 (tpp) cc_final: 0.6626 (tpp) REVERT: D 54 PHE cc_start: 0.6078 (OUTLIER) cc_final: 0.5754 (t80) REVERT: D 246 GLN cc_start: 0.6766 (tp40) cc_final: 0.6430 (tp-100) REVERT: D 255 LYS cc_start: 0.8038 (tptt) cc_final: 0.7699 (mmtm) REVERT: E 21 GLU cc_start: 0.8004 (pt0) cc_final: 0.7618 (pm20) REVERT: E 105 ARG cc_start: 0.7723 (ptp-170) cc_final: 0.7131 (ptp-170) REVERT: E 119 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.5978 (pm20) REVERT: F 53 ARG cc_start: 0.8834 (ptp-110) cc_final: 0.8286 (mtm110) REVERT: F 61 ARG cc_start: 0.8542 (ptp90) cc_final: 0.8127 (ptm-80) REVERT: F 91 ARG cc_start: 0.6771 (ptm-80) cc_final: 0.5924 (ptm-80) REVERT: F 139 MET cc_start: 0.2773 (OUTLIER) cc_final: 0.2309 (ppp) REVERT: F 144 PHE cc_start: 0.8771 (t80) cc_final: 0.8403 (t80) REVERT: F 148 CYS cc_start: 0.9049 (m) cc_final: 0.8831 (m) REVERT: G 13 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7698 (mttp) REVERT: G 87 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.6970 (pp) REVERT: G 125 GLN cc_start: 0.7077 (tm-30) cc_final: 0.6831 (tm-30) REVERT: H 27 CYS cc_start: 0.8193 (t) cc_final: 0.7710 (p) REVERT: H 117 LYS cc_start: 0.7627 (ptmm) cc_final: 0.6927 (mttt) REVERT: H 119 MET cc_start: 0.5950 (mtp) cc_final: 0.5717 (mtm) REVERT: H 131 GLN cc_start: 0.6524 (tm-30) cc_final: 0.6310 (tm-30) outliers start: 86 outliers final: 64 residues processed: 390 average time/residue: 0.1666 time to fit residues: 98.4626 Evaluate side-chains 370 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 114 optimal weight: 0.9990 chunk 167 optimal weight: 0.0170 chunk 137 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 166 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 233 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 ASN B 152 GLN D 125 ASN E 72 GLN E 213 HIS F 38 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.191579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.157029 restraints weight = 34004.367| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.43 r_work: 0.3998 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21027 Z= 0.128 Angle : 0.647 10.939 28454 Z= 0.323 Chirality : 0.043 0.239 3311 Planarity : 0.004 0.074 3643 Dihedral : 8.776 175.311 2960 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.45 % Allowed : 21.12 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2601 helix: 0.79 (0.15), residues: 1239 sheet: -0.41 (0.23), residues: 495 loop : -0.70 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 52 TYR 0.025 0.001 TYR E 254 PHE 0.035 0.001 PHE E 339 TRP 0.010 0.001 TRP F 28 HIS 0.003 0.001 HIS E 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21027) covalent geometry : angle 0.64682 / 0.32 (28454) hydrogen bonds : bond 0.03337 / 2.20 ( 1103) hydrogen bonds : angle 4.45327 / 3.13 ( 3177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 318 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6503 (pm20) REVERT: A 307 TRP cc_start: 0.7310 (t60) cc_final: 0.6600 (t60) REVERT: A 409 PHE cc_start: 0.8302 (t80) cc_final: 0.7659 (m-80) REVERT: A 851 GLU cc_start: 0.8788 (tp30) cc_final: 0.8229 (mm-30) REVERT: A 853 MET cc_start: 0.9296 (mmm) cc_final: 0.9078 (mmp) REVERT: B 193 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7276 (mm) REVERT: B 210 ARG cc_start: 0.7379 (ttp80) cc_final: 0.6805 (ttp80) REVERT: B 229 MET cc_start: 0.6956 (tpp) cc_final: 0.6678 (tpp) REVERT: D 246 GLN cc_start: 0.6875 (tp40) cc_final: 0.6533 (tp-100) REVERT: D 255 LYS cc_start: 0.8199 (tptt) cc_final: 0.7734 (mmtm) REVERT: E 21 GLU cc_start: 0.8211 (pt0) cc_final: 0.7750 (pm20) REVERT: E 105 ARG cc_start: 0.7852 (ptp-170) cc_final: 0.7199 (ptp-170) REVERT: E 119 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.6064 (pm20) REVERT: F 53 ARG cc_start: 0.8925 (ptp-110) cc_final: 0.8557 (mtm110) REVERT: F 144 PHE cc_start: 0.8853 (t80) cc_final: 0.8572 (t80) REVERT: F 148 CYS cc_start: 0.9036 (m) cc_final: 0.8828 (m) REVERT: G 13 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7776 (mttp) REVERT: G 87 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7049 (pp) REVERT: G 125 GLN cc_start: 0.7191 (tm-30) cc_final: 0.6928 (tm-30) REVERT: H 27 CYS cc_start: 0.8290 (t) cc_final: 0.7741 (p) REVERT: H 131 GLN cc_start: 0.6602 (tm-30) cc_final: 0.5973 (tm-30) outliers start: 79 outliers final: 67 residues processed: 373 average time/residue: 0.1634 time to fit residues: 93.0685 Evaluate side-chains 375 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 304 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 17 optimal weight: 7.9990 chunk 237 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 0.0060 chunk 30 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 233 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 239 optimal weight: 0.4980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 ASN D 125 ASN E 194 HIS E 213 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.192314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.157840 restraints weight = 34052.812| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.49 r_work: 0.4017 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21027 Z= 0.120 Angle : 0.647 9.818 28454 Z= 0.323 Chirality : 0.043 0.228 3311 Planarity : 0.004 0.074 3643 Dihedral : 8.713 174.589 2960 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.84 % Allowed : 21.73 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2601 helix: 0.86 (0.15), residues: 1237 sheet: -0.39 (0.23), residues: 495 loop : -0.66 (0.23), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 140 TYR 0.020 0.001 TYR B 213 PHE 0.051 0.002 PHE E 339 TRP 0.011 0.001 TRP F 28 HIS 0.006 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (21027) covalent geometry : angle 0.64702 / 0.32 (28454) hydrogen bonds : bond 0.03270 / 2.15 ( 1103) hydrogen bonds : angle 4.40482 / 3.10 ( 3177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 329 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8260 (t80) cc_final: 0.7597 (m-80) REVERT: A 851 GLU cc_start: 0.8754 (tp30) cc_final: 0.8204 (mm-30) REVERT: A 853 MET cc_start: 0.9280 (mmm) cc_final: 0.9067 (mmp) REVERT: B 102 MET cc_start: 0.7820 (tpp) cc_final: 0.7002 (tpt) REVERT: B 152 GLN cc_start: 0.7437 (tp-100) cc_final: 0.7217 (pt0) REVERT: B 155 ARG cc_start: 0.7400 (mtp85) cc_final: 0.6763 (mtp85) REVERT: B 210 ARG cc_start: 0.7328 (ttp80) cc_final: 0.6753 (ttp80) REVERT: B 229 MET cc_start: 0.6830 (tpp) cc_final: 0.6563 (tpp) REVERT: D 246 GLN cc_start: 0.6833 (tp40) cc_final: 0.6509 (tp-100) REVERT: D 255 LYS cc_start: 0.8192 (tptt) cc_final: 0.7720 (mmtm) REVERT: E 21 GLU cc_start: 0.8168 (pt0) cc_final: 0.7703 (pm20) REVERT: E 105 ARG cc_start: 0.7795 (ptp-170) cc_final: 0.7460 (ptp-170) REVERT: F 53 ARG cc_start: 0.8871 (ptp-110) cc_final: 0.8545 (mtm110) REVERT: F 61 ARG cc_start: 0.8593 (ptp90) cc_final: 0.8360 (ptp90) REVERT: F 99 LEU cc_start: 0.7842 (tp) cc_final: 0.7547 (pp) REVERT: F 139 MET cc_start: 0.2382 (ppp) cc_final: 0.1919 (ppp) REVERT: F 144 PHE cc_start: 0.8853 (t80) cc_final: 0.8477 (t80) REVERT: F 148 CYS cc_start: 0.9042 (m) cc_final: 0.8819 (m) REVERT: F 214 PHE cc_start: 0.8668 (m-10) cc_final: 0.8250 (m-80) REVERT: G 13 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7764 (mttp) REVERT: G 87 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.6952 (pp) REVERT: G 125 GLN cc_start: 0.7183 (tm-30) cc_final: 0.6915 (tm-30) REVERT: G 199 MET cc_start: 0.3442 (ptt) cc_final: 0.3123 (ptt) REVERT: H 27 CYS cc_start: 0.8146 (t) cc_final: 0.7556 (p) REVERT: H 117 LYS cc_start: 0.7604 (ptmm) cc_final: 0.7018 (mttt) outliers start: 65 outliers final: 58 residues processed: 373 average time/residue: 0.1510 time to fit residues: 86.7844 Evaluate side-chains 372 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 313 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 14 optimal weight: 20.0000 chunk 112 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 236 optimal weight: 0.4980 chunk 251 optimal weight: 0.2980 chunk 132 optimal weight: 0.1980 chunk 185 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 70 optimal weight: 0.0470 chunk 43 optimal weight: 0.0470 overall best weight: 0.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN A 655 ASN D 125 ASN D 358 GLN E 213 HIS G 36 ASN G 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.194393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.160304 restraints weight = 34154.013| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.48 r_work: 0.4051 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3912 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21027 Z= 0.115 Angle : 0.650 9.918 28454 Z= 0.322 Chirality : 0.043 0.211 3311 Planarity : 0.004 0.070 3643 Dihedral : 8.586 172.806 2960 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.75 % Allowed : 21.95 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2601 helix: 0.97 (0.15), residues: 1240 sheet: -0.35 (0.23), residues: 483 loop : -0.58 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 140 TYR 0.015 0.001 TYR B 279 PHE 0.033 0.002 PHE E 339 TRP 0.014 0.001 TRP F 28 HIS 0.005 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (21027) covalent geometry : angle 0.65049 / 0.32 (28454) hydrogen bonds : bond 0.03101 / 2.05 ( 1103) hydrogen bonds : angle 4.30327 / 3.02 ( 3177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5703.48 seconds wall clock time: 98 minutes 39.06 seconds (5919.06 seconds total)