Starting phenix.real_space_refine on Sun Oct 12 06:03:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umy_42388/10_2025/8umy_42388_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umy_42388/10_2025/8umy_42388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8umy_42388/10_2025/8umy_42388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umy_42388/10_2025/8umy_42388.map" model { file = "/net/cci-nas-00/data/ceres_data/8umy_42388/10_2025/8umy_42388_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umy_42388/10_2025/8umy_42388_neut.cif" } resolution = 2.83 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= 0.083 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 61 5.49 5 Mg 4 5.21 5 S 138 5.16 5 C 13599 2.51 5 N 3772 2.21 5 O 4286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21860 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4319 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 512} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2591 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2541 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} 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: "I" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" 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: "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: 4.57, per 1000 atoms: 0.21 Number of scatterers: 21860 At special positions: 0 Unit cell: (117.576, 128.34, 138.276, 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 138 16.00 P 61 15.00 Mg 4 11.99 O 4286 8.00 N 3772 7.00 C 13599 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: 1.57 Conformation dependent library (CDL) restraints added in 905.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5038 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 14 sheets defined 51.3% alpha, 14.4% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.552A pdb=" N GLU A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 437 through 440 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.964A pdb=" N GLN A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.908A pdb=" N SER A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.771A pdb=" N VAL A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 627 through 643 removed outlier: 4.122A pdb=" N GLY A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 656 Processing helix chain 'A' and resid 666 through 687 Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.835A pdb=" N LEU A 694 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 695 " --> pdb=" O PHE A 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 695' Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.469A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 742 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.554A 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 762 through 769 Processing helix chain 'A' and resid 777 through 781 Processing helix chain 'A' and resid 782 through 799 removed outlier: 3.785A pdb=" N TYR A 799 " --> pdb=" O THR A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 837 through 863 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.614A pdb=" N ILE B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.542A pdb=" N VAL B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.679A pdb=" N ARG B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 194 through 210 removed outlier: 3.649A pdb=" N ARG B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) 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 255 removed outlier: 3.982A pdb=" N VAL B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 removed outlier: 3.622A pdb=" N VAL B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.912A 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 350 removed outlier: 3.732A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.678A pdb=" N LEU C 34 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 65 through 78 removed outlier: 3.520A pdb=" N ILE C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 138 through 145 removed outlier: 3.607A pdb=" N PHE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.559A 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 194 removed outlier: 3.791A pdb=" N VAL C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 removed outlier: 4.025A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.645A pdb=" N GLN C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 291 removed outlier: 3.788A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.873A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 83 through 96 removed outlier: 3.581A pdb=" N ILE D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 115 through 128 removed outlier: 3.840A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 removed outlier: 3.529A pdb=" N ALA D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 187 through 194 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 235 removed outlier: 4.016A pdb=" N GLU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.876A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.644A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 removed outlier: 3.592A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 362 removed outlier: 4.265A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 4.201A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.862A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 30 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 66 removed outlier: 4.019A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 6.848A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 117 removed outlier: 3.553A pdb=" N VAL E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 149 removed outlier: 3.682A pdb=" N ARG E 149 " --> pdb=" O GLN E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.761A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.618A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.775A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.676A pdb=" N HIS E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.150A 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 72 through 80 removed outlier: 3.699A pdb=" N LYS F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.721A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.601A pdb=" N LYS G 13 " --> pdb=" O GLY G 9 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 81 removed outlier: 3.532A pdb=" N LYS G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 151 Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 219 No H-bonds generated for 'chain 'G' and resid 217 through 219' Processing helix chain 'H' and resid 9 through 14 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 76 removed outlier: 3.595A pdb=" N SER H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 72 through 76' Processing helix chain 'H' and resid 141 through 151 removed outlier: 3.666A pdb=" N ARG H 146 " --> pdb=" O GLY H 142 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS H 148 " --> pdb=" O PHE H 144 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 154 No H-bonds generated for 'chain 'H' and resid 152 through 154' Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.562A pdb=" N GLU H 193 " --> pdb=" O LYS H 190 " (cutoff:3.500A) removed outlier: 3.749A 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 216 Processing helix chain 'H' and resid 217 through 219 No H-bonds generated for 'chain 'H' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 398 removed outlier: 5.959A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N MET A 398 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ALA A 370 " --> pdb=" O CYS A 488 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N CYS A 490 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU A 372 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 369 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU A 508 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 371 " --> pdb=" O LEU A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 803 through 807 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.046A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.448A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.188A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.620A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N CYS E 165 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E 40 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N HIS E 37 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL E 182 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 57 through 62 removed outlier: 6.600A pdb=" N ARG F 5 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR F 60 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU F 3 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 182 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL G 167 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 205 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 71 removed outlier: 7.095A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 168 through 170 Processing sheet with id=AB2, first strand: chain 'G' and resid 60 through 62 removed outlier: 3.810A pdb=" N VAL G 111 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS H 181 " --> pdb=" O VAL G 111 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL H 203 " --> pdb=" O CYS H 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.732A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 59 through 62 removed outlier: 3.888A pdb=" N THR H 59 " --> pdb=" O ARG H 5 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR H 114 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 67 through 71 removed outlier: 3.536A pdb=" N VAL H 70 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR H 196 " --> pdb=" O LYS H 138 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 3039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 2.21 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: 7228 1.36 - 1.50: 5630 1.50 - 1.65: 9243 1.65 - 1.80: 78 1.80 - 1.95: 130 Bond restraints: 22309 Sorted by residual: bond pdb=" CA SER F 10 " pdb=" CB SER F 10 " ideal model delta sigma weight residual 1.528 1.476 0.053 1.59e-02 3.96e+03 1.10e+01 bond pdb=" N VAL B 331 " pdb=" CA VAL B 331 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.62e+00 bond pdb=" N GLU A 592 " pdb=" CA GLU A 592 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.28e-02 6.10e+03 7.01e+00 bond pdb=" N MET F 244 " pdb=" CA MET F 244 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.26e-02 6.30e+03 6.81e+00 bond pdb=" N MET A 483 " pdb=" CA MET A 483 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.40e-02 5.10e+03 6.67e+00 ... (remaining 22304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 29491 1.58 - 3.16: 758 3.16 - 4.74: 98 4.74 - 6.32: 38 6.32 - 7.90: 13 Bond angle restraints: 30398 Sorted by residual: angle pdb=" N VAL E 235 " pdb=" CA VAL E 235 " pdb=" C VAL E 235 " ideal model delta sigma weight residual 112.35 104.45 7.90 1.41e+00 5.03e-01 3.14e+01 angle pdb=" N ARG E 234 " pdb=" CA ARG E 234 " pdb=" C ARG E 234 " ideal model delta sigma weight residual 113.50 107.43 6.07 1.23e+00 6.61e-01 2.44e+01 angle pdb=" N ILE F 11 " pdb=" CA ILE F 11 " pdb=" CB ILE F 11 " ideal model delta sigma weight residual 110.51 105.16 5.35 1.11e+00 8.12e-01 2.32e+01 angle pdb=" CA ASN B 332 " pdb=" CB ASN B 332 " pdb=" CG ASN B 332 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.05e+01 angle pdb=" C ILE F 11 " pdb=" CA ILE F 11 " pdb=" CB ILE F 11 " ideal model delta sigma weight residual 111.88 106.24 5.64 1.28e+00 6.10e-01 1.94e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.58: 12954 28.58 - 57.16: 636 57.16 - 85.74: 42 85.74 - 114.32: 1 114.32 - 142.90: 2 Dihedral angle restraints: 13635 sinusoidal: 5895 harmonic: 7740 Sorted by residual: dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 157.10 142.90 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" CA GLU A 818 " pdb=" C GLU A 818 " pdb=" N PRO A 819 " pdb=" CA PRO A 819 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA LEU E 148 " pdb=" C LEU E 148 " pdb=" N ARG E 149 " pdb=" CA ARG E 149 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 13632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3298 0.086 - 0.173: 230 0.173 - 0.259: 5 0.259 - 0.345: 2 0.345 - 0.432: 1 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CA ILE F 11 " pdb=" N ILE F 11 " pdb=" C ILE F 11 " pdb=" CB ILE F 11 " both_signs ideal model delta sigma weight residual False 2.43 2.86 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA GLU A 592 " pdb=" N GLU A 592 " pdb=" C GLU A 592 " pdb=" CB GLU A 592 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CB ILE F 11 " pdb=" CA ILE F 11 " pdb=" CG1 ILE F 11 " pdb=" CG2 ILE F 11 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3533 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO A 699 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 234 " -0.284 9.50e-02 1.11e+02 1.27e-01 9.95e+00 pdb=" NE ARG E 234 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG E 234 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG E 234 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 234 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 198 " 0.254 9.50e-02 1.11e+02 1.14e-01 7.98e+00 pdb=" NE ARG D 198 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG D 198 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG D 198 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 198 " 0.010 2.00e-02 2.50e+03 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 265 2.64 - 3.21: 18030 3.21 - 3.77: 34623 3.77 - 4.34: 47607 4.34 - 4.90: 78709 Nonbonded interactions: 179234 Sorted by model distance: nonbonded pdb=" OG1 THR C 67 " pdb="MG MG C 401 " model vdw 2.080 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.087 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR D 85 " pdb="MG MG D 401 " model vdw 2.094 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.098 2.170 ... (remaining 179229 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.780 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.003 0.063 22309 Z= 0.172 Angle : 0.633 7.896 30398 Z= 0.366 Chirality : 0.044 0.432 3536 Planarity : 0.007 0.127 3723 Dihedral : 15.227 142.900 8597 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.34 % Allowed : 8.83 % Favored : 88.83 % Cbeta Deviations : 0.04 % 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 aren not related in a simple way. whole: -1.84 (0.14), residues: 2623 helix: -1.59 (0.12), residues: 1230 sheet: -0.32 (0.22), residues: 532 loop : -0.84 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 198 TYR 0.024 0.001 TYR E 238 PHE 0.016 0.001 PHE A 632 TRP 0.006 0.001 TRP A 590 HIS 0.002 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00311 (22309) covalent geometry : angle 0.63305 (30398) hydrogen bonds : bond 0.18962 ( 1094) hydrogen bonds : angle 6.76354 ( 3123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 464 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 HIS cc_start: 0.6660 (m170) cc_final: 0.6173 (m90) REVERT: A 313 LEU cc_start: 0.8558 (mm) cc_final: 0.8169 (tm) REVERT: A 353 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8277 (tm-30) REVERT: A 592 GLU cc_start: 0.7777 (tp30) cc_final: 0.7540 (tt0) REVERT: A 767 ASP cc_start: 0.7793 (t70) cc_final: 0.7510 (t70) REVERT: B 100 ASP cc_start: 0.8106 (m-30) cc_final: 0.7868 (m-30) REVERT: B 148 ASP cc_start: 0.7971 (t70) cc_final: 0.7756 (t0) REVERT: B 159 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7052 (mm-30) REVERT: B 229 MET cc_start: 0.8843 (tpt) cc_final: 0.8595 (tpp) REVERT: B 301 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.7102 (mtm110) REVERT: C 307 ASP cc_start: 0.7709 (m-30) cc_final: 0.7488 (m-30) REVERT: D 47 LYS cc_start: 0.8445 (mmtm) cc_final: 0.8232 (mmtt) REVERT: D 102 ARG cc_start: 0.7982 (ptp-170) cc_final: 0.7686 (mpp-170) REVERT: D 157 SER cc_start: 0.9184 (m) cc_final: 0.8953 (p) REVERT: D 185 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8200 (mtt-85) REVERT: D 265 ILE cc_start: 0.8350 (tt) cc_final: 0.7808 (tt) REVERT: E 298 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7563 (tm-30) REVERT: E 304 ASP cc_start: 0.7389 (t0) cc_final: 0.7110 (t70) REVERT: F 20 LYS cc_start: 0.8307 (tptm) cc_final: 0.8091 (tptp) REVERT: F 146 ARG cc_start: 0.7942 (tpm170) cc_final: 0.7372 (tpm170) REVERT: F 150 ASP cc_start: 0.7564 (m-30) cc_final: 0.7029 (m-30) REVERT: F 197 ILE cc_start: 0.6305 (mm) cc_final: 0.5901 (tp) REVERT: F 241 ILE cc_start: 0.7503 (mm) cc_final: 0.6805 (mt) REVERT: F 248 LYS cc_start: 0.8793 (ptpt) cc_final: 0.8367 (pttm) REVERT: G 1 MET cc_start: 0.5900 (tpt) cc_final: 0.5527 (tpt) REVERT: G 8 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7671 (tm-30) REVERT: G 91 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7909 (mtm-85) REVERT: G 243 ASP cc_start: 0.7039 (t0) cc_final: 0.6698 (t0) REVERT: G 246 HIS cc_start: 0.7254 (p90) cc_final: 0.6968 (p90) REVERT: G 248 LYS cc_start: 0.8597 (mttt) cc_final: 0.7919 (mttt) REVERT: H 40 MET cc_start: 0.6980 (ttp) cc_final: 0.6687 (mtp) REVERT: H 116 MET cc_start: 0.5727 (mmt) cc_final: 0.5351 (mtm) REVERT: H 140 PRO cc_start: 0.8779 (Cg_exo) cc_final: 0.8490 (Cg_endo) outliers start: 54 outliers final: 17 residues processed: 499 average time/residue: 0.6019 time to fit residues: 340.3810 Evaluate side-chains 365 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 347 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain E residue 234 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 206 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 GLN A 727 GLN B 48 ASN B 125 GLN B 182 GLN B 268 GLN B 332 ASN B 346 GLN C 29 GLN C 330 GLN D 246 GLN E 102 ASN E 120 GLN F 49 GLN H 125 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.172319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126136 restraints weight = 25811.662| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.11 r_work: 0.3350 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22309 Z= 0.118 Angle : 0.531 7.389 30398 Z= 0.278 Chirality : 0.040 0.220 3536 Planarity : 0.005 0.080 3723 Dihedral : 14.292 147.742 3484 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.07 % Allowed : 15.02 % Favored : 81.90 % 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 aren not related in a simple way. whole: -0.43 (0.16), residues: 2623 helix: 0.06 (0.14), residues: 1248 sheet: -0.29 (0.22), residues: 539 loop : -0.51 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 52 TYR 0.016 0.001 TYR E 238 PHE 0.023 0.001 PHE A 632 TRP 0.005 0.001 TRP G 28 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00256 (22309) covalent geometry : angle 0.53150 (30398) hydrogen bonds : bond 0.03762 ( 1094) hydrogen bonds : angle 4.55880 ( 3123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 370 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 362 SER cc_start: 0.6633 (m) cc_final: 0.6379 (m) REVERT: A 499 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7750 (mtp85) REVERT: A 546 ASP cc_start: 0.8374 (t0) cc_final: 0.7807 (t0) REVERT: A 767 ASP cc_start: 0.8225 (t70) cc_final: 0.8017 (t70) REVERT: A 834 LYS cc_start: 0.8237 (tttt) cc_final: 0.7968 (mmtp) REVERT: B 159 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7416 (mm-30) REVERT: B 301 ARG cc_start: 0.7817 (ttm-80) cc_final: 0.7565 (mtm110) REVERT: D 47 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8434 (mmtt) REVERT: D 185 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8267 (mtt-85) REVERT: D 290 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7631 (mm-30) REVERT: D 316 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6783 (mm-30) REVERT: D 333 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7860 (mt-10) REVERT: E 112 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8730 (tp) REVERT: E 298 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7764 (tm-30) REVERT: E 333 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: F 19 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7464 (pp) REVERT: F 20 LYS cc_start: 0.8431 (tptm) cc_final: 0.8230 (tptp) REVERT: F 49 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8034 (tm130) REVERT: F 146 ARG cc_start: 0.8251 (tpm170) cc_final: 0.7515 (tpm170) REVERT: F 150 ASP cc_start: 0.7753 (m-30) cc_final: 0.6920 (m-30) REVERT: F 197 ILE cc_start: 0.6540 (mm) cc_final: 0.6112 (tp) REVERT: F 248 LYS cc_start: 0.8697 (ptpt) cc_final: 0.8487 (ptpt) REVERT: G 53 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6359 (mmm160) REVERT: G 132 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7158 (pt0) REVERT: G 203 VAL cc_start: 0.8455 (p) cc_final: 0.8237 (m) REVERT: G 248 LYS cc_start: 0.8891 (mttt) cc_final: 0.8452 (mttt) REVERT: H 40 MET cc_start: 0.6982 (ttp) cc_final: 0.6659 (mtp) REVERT: H 93 GLU cc_start: 0.6413 (mm-30) cc_final: 0.4965 (mp0) REVERT: H 116 MET cc_start: 0.5968 (mmt) cc_final: 0.5304 (mtm) REVERT: H 140 PRO cc_start: 0.8479 (Cg_exo) cc_final: 0.7002 (Cg_endo) REVERT: H 143 GLU cc_start: 0.7967 (pp20) cc_final: 0.7343 (pp20) outliers start: 71 outliers final: 34 residues processed: 411 average time/residue: 0.6110 time to fit residues: 285.4715 Evaluate side-chains 368 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 325 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 252 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN A 630 GLN B 48 ASN B 332 ASN C 256 ASN C 285 HIS D 246 GLN F 38 GLN F 71 ASN G 177 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123069 restraints weight = 25979.954| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.09 r_work: 0.3302 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22309 Z= 0.145 Angle : 0.541 11.133 30398 Z= 0.279 Chirality : 0.041 0.157 3536 Planarity : 0.004 0.073 3723 Dihedral : 14.135 150.854 3466 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.38 % Allowed : 15.89 % Favored : 80.74 % 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 aren not related in a simple way. whole: 0.08 (0.16), residues: 2623 helix: 0.68 (0.15), residues: 1249 sheet: -0.37 (0.21), residues: 544 loop : -0.38 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 15 TYR 0.037 0.001 TYR E 238 PHE 0.020 0.001 PHE A 632 TRP 0.007 0.001 TRP E 251 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00338 (22309) covalent geometry : angle 0.54065 (30398) hydrogen bonds : bond 0.03556 ( 1094) hydrogen bonds : angle 4.24213 ( 3123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 340 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8312 (tm-30) REVERT: A 362 SER cc_start: 0.6634 (m) cc_final: 0.6366 (m) REVERT: A 435 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8545 (m-30) REVERT: A 499 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7799 (mtp85) REVERT: A 546 ASP cc_start: 0.8411 (t0) cc_final: 0.7855 (t0) REVERT: A 591 GLN cc_start: 0.8339 (mt0) cc_final: 0.8072 (mp10) REVERT: A 834 LYS cc_start: 0.8231 (tttt) cc_final: 0.7964 (mmtp) REVERT: A 847 GLU cc_start: 0.8167 (tt0) cc_final: 0.7883 (tp30) REVERT: B 301 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7540 (mtm110) REVERT: B 331 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8369 (m) REVERT: D 185 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8321 (mtt-85) REVERT: D 290 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7618 (mm-30) REVERT: D 356 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8589 (ttm) REVERT: E 83 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: E 210 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: E 298 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7761 (tm-30) REVERT: E 333 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: F 19 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7368 (pp) REVERT: F 49 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7995 (tp40) REVERT: F 87 ILE cc_start: 0.7995 (mt) cc_final: 0.7637 (pp) REVERT: F 146 ARG cc_start: 0.8244 (tpm170) cc_final: 0.7510 (tpm170) REVERT: F 150 ASP cc_start: 0.7787 (m-30) cc_final: 0.6899 (m-30) REVERT: F 197 ILE cc_start: 0.6925 (mm) cc_final: 0.6445 (tp) REVERT: F 199 MET cc_start: 0.7998 (ppp) cc_final: 0.7662 (ppp) REVERT: F 240 LYS cc_start: 0.8072 (tmtm) cc_final: 0.7816 (tmtm) REVERT: G 41 ASP cc_start: 0.8797 (p0) cc_final: 0.8040 (p0) REVERT: G 53 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6481 (mmm160) REVERT: G 132 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7208 (pt0) REVERT: G 203 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8301 (m) REVERT: G 248 LYS cc_start: 0.8822 (mttt) cc_final: 0.8460 (mttt) REVERT: H 40 MET cc_start: 0.7052 (ttp) cc_final: 0.6744 (mtp) REVERT: H 93 GLU cc_start: 0.6296 (mm-30) cc_final: 0.4871 (mp0) REVERT: H 116 MET cc_start: 0.6148 (mmt) cc_final: 0.5362 (mtm) outliers start: 78 outliers final: 41 residues processed: 391 average time/residue: 0.6380 time to fit residues: 282.0185 Evaluate side-chains 368 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 315 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 146 ARG Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 114 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 504 GLN B 48 ASN B 332 ASN C 37 HIS C 317 ASN D 117 GLN D 308 ASN E 265 GLN F 38 GLN F 71 ASN G 8 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.166624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119720 restraints weight = 26001.609| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.12 r_work: 0.3250 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22309 Z= 0.184 Angle : 0.575 11.020 30398 Z= 0.295 Chirality : 0.042 0.169 3536 Planarity : 0.004 0.073 3723 Dihedral : 14.212 155.834 3466 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.94 % Allowed : 16.15 % Favored : 79.91 % 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 aren not related in a simple way. whole: 0.28 (0.16), residues: 2623 helix: 0.89 (0.15), residues: 1250 sheet: -0.37 (0.21), residues: 545 loop : -0.29 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 52 TYR 0.029 0.002 TYR E 238 PHE 0.018 0.002 PHE A 632 TRP 0.009 0.001 TRP E 251 HIS 0.005 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00439 (22309) covalent geometry : angle 0.57517 (30398) hydrogen bonds : bond 0.03710 ( 1094) hydrogen bonds : angle 4.16588 ( 3123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 332 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8299 (tm-30) REVERT: A 499 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7813 (mtp85) REVERT: A 546 ASP cc_start: 0.8353 (t0) cc_final: 0.7803 (t0) REVERT: A 834 LYS cc_start: 0.8207 (tttt) cc_final: 0.7987 (mppt) REVERT: B 301 ARG cc_start: 0.7819 (ttm-80) cc_final: 0.7469 (mtm110) REVERT: B 331 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8534 (m) REVERT: D 185 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8353 (mtt-85) REVERT: D 290 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: D 316 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6975 (mm-30) REVERT: D 356 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8558 (ttp) REVERT: E 83 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: E 210 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: E 298 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7696 (tm-30) REVERT: E 333 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: F 17 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: F 19 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7405 (pp) REVERT: F 87 ILE cc_start: 0.8048 (mt) cc_final: 0.7811 (pp) REVERT: F 146 ARG cc_start: 0.8230 (tpm170) cc_final: 0.7550 (tpm170) REVERT: F 150 ASP cc_start: 0.7861 (m-30) cc_final: 0.7091 (m-30) REVERT: F 199 MET cc_start: 0.8100 (ppp) cc_final: 0.7804 (ppp) REVERT: G 53 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6493 (mmm160) REVERT: G 115 GLU cc_start: 0.7867 (mp0) cc_final: 0.7271 (mp0) REVERT: G 132 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7213 (pt0) REVERT: G 248 LYS cc_start: 0.8846 (mttt) cc_final: 0.8348 (mttt) REVERT: H 40 MET cc_start: 0.7143 (ttp) cc_final: 0.6816 (mtp) REVERT: H 93 GLU cc_start: 0.6227 (mm-30) cc_final: 0.4792 (mp0) REVERT: H 116 MET cc_start: 0.6249 (mmt) cc_final: 0.5352 (mtm) outliers start: 91 outliers final: 50 residues processed: 398 average time/residue: 0.6272 time to fit residues: 282.9135 Evaluate side-chains 376 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 314 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 224 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 60 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 201 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 197 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 332 ASN C 38 GLN D 117 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 38 GLN F 71 ASN F 246 HIS G 8 GLN G 71 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.166198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123286 restraints weight = 25925.937| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.96 r_work: 0.3265 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22309 Z= 0.183 Angle : 0.579 11.597 30398 Z= 0.295 Chirality : 0.042 0.165 3536 Planarity : 0.004 0.073 3723 Dihedral : 14.245 157.630 3465 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.81 % Allowed : 17.53 % Favored : 78.66 % 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 aren not related in a simple way. whole: 0.39 (0.16), residues: 2623 helix: 0.98 (0.15), residues: 1253 sheet: -0.33 (0.21), residues: 544 loop : -0.23 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 52 TYR 0.029 0.002 TYR E 238 PHE 0.018 0.002 PHE A 632 TRP 0.008 0.001 TRP E 251 HIS 0.005 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00438 (22309) covalent geometry : angle 0.57935 (30398) hydrogen bonds : bond 0.03651 ( 1094) hydrogen bonds : angle 4.13265 ( 3123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 322 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8287 (tm-30) REVERT: A 499 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7727 (mtp85) REVERT: A 546 ASP cc_start: 0.8342 (t0) cc_final: 0.7757 (t0) REVERT: A 591 GLN cc_start: 0.8198 (mt0) cc_final: 0.7826 (mp10) REVERT: A 834 LYS cc_start: 0.8208 (tttt) cc_final: 0.7942 (mppt) REVERT: A 843 LEU cc_start: 0.7965 (tp) cc_final: 0.7094 (tp) REVERT: B 264 LYS cc_start: 0.7931 (tmtp) cc_final: 0.7679 (ttpp) REVERT: B 301 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7380 (mtm110) REVERT: B 331 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8465 (m) REVERT: C 196 ASP cc_start: 0.8155 (p0) cc_final: 0.7765 (p0) REVERT: D 102 ARG cc_start: 0.8496 (ptp-170) cc_final: 0.7994 (mpp-170) REVERT: D 185 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8282 (mtt-85) REVERT: D 290 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7491 (mm-30) REVERT: D 316 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7001 (mm-30) REVERT: E 83 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: E 210 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: E 239 PRO cc_start: 0.7098 (Cg_exo) cc_final: 0.6803 (Cg_endo) REVERT: E 298 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 333 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8523 (tt0) REVERT: F 17 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: F 19 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7129 (pp) REVERT: F 87 ILE cc_start: 0.7873 (mt) cc_final: 0.7508 (pp) REVERT: F 146 ARG cc_start: 0.8222 (tpm170) cc_final: 0.7498 (tpm170) REVERT: F 150 ASP cc_start: 0.7863 (m-30) cc_final: 0.7053 (m-30) REVERT: G 41 ASP cc_start: 0.8805 (p0) cc_final: 0.8072 (p0) REVERT: G 53 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6388 (mmm160) REVERT: G 115 GLU cc_start: 0.7834 (mp0) cc_final: 0.7195 (mp0) REVERT: G 132 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7199 (pt0) REVERT: G 143 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: G 238 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8201 (tp30) REVERT: G 248 LYS cc_start: 0.8821 (mttt) cc_final: 0.8218 (mttt) REVERT: H 40 MET cc_start: 0.7214 (ttp) cc_final: 0.6955 (mtp) REVERT: H 93 GLU cc_start: 0.6225 (mm-30) cc_final: 0.4773 (mp0) REVERT: H 116 MET cc_start: 0.6366 (mmt) cc_final: 0.5346 (mtm) outliers start: 88 outliers final: 54 residues processed: 380 average time/residue: 0.6455 time to fit residues: 278.1951 Evaluate side-chains 378 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 311 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 224 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 208 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 115 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 190 optimal weight: 0.5980 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 332 ASN D 117 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 38 GLN F 49 GLN F 71 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.165899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119244 restraints weight = 25925.727| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.11 r_work: 0.3244 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22309 Z= 0.180 Angle : 0.590 11.893 30398 Z= 0.299 Chirality : 0.042 0.151 3536 Planarity : 0.004 0.074 3723 Dihedral : 14.281 159.219 3464 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.94 % Allowed : 17.58 % Favored : 78.48 % 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 aren not related in a simple way. whole: 0.46 (0.16), residues: 2623 helix: 1.06 (0.15), residues: 1252 sheet: -0.31 (0.21), residues: 540 loop : -0.22 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 52 TYR 0.023 0.002 TYR E 238 PHE 0.017 0.002 PHE A 632 TRP 0.008 0.001 TRP E 251 HIS 0.005 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00429 (22309) covalent geometry : angle 0.58992 (30398) hydrogen bonds : bond 0.03609 ( 1094) hydrogen bonds : angle 4.09029 ( 3123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 327 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8310 (tm-30) REVERT: A 435 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8630 (m-30) REVERT: A 499 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7748 (mtp85) REVERT: A 546 ASP cc_start: 0.8280 (t0) cc_final: 0.7749 (t0) REVERT: A 803 TYR cc_start: 0.8407 (m-80) cc_final: 0.7916 (m-80) REVERT: A 834 LYS cc_start: 0.8153 (tttt) cc_final: 0.7950 (mppt) REVERT: A 843 LEU cc_start: 0.8131 (tp) cc_final: 0.7744 (tp) REVERT: A 847 GLU cc_start: 0.8314 (mp0) cc_final: 0.8085 (pm20) REVERT: A 855 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6729 (ttp80) REVERT: B 264 LYS cc_start: 0.8107 (tmtp) cc_final: 0.7785 (tmmt) REVERT: B 301 ARG cc_start: 0.7807 (ttm-80) cc_final: 0.7538 (mtm110) REVERT: B 331 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8590 (m) REVERT: C 196 ASP cc_start: 0.8211 (p0) cc_final: 0.7823 (p0) REVERT: D 102 ARG cc_start: 0.8498 (ptp-170) cc_final: 0.8202 (mpp-170) REVERT: D 185 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8315 (mtt-85) REVERT: D 290 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: D 316 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: E 83 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: E 210 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: E 298 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7633 (tm-30) REVERT: E 333 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: F 17 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: F 19 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7305 (pp) REVERT: F 49 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7912 (tm130) REVERT: F 87 ILE cc_start: 0.7814 (mt) cc_final: 0.7490 (pp) REVERT: F 128 ILE cc_start: 0.5787 (OUTLIER) cc_final: 0.5357 (pp) REVERT: F 146 ARG cc_start: 0.8244 (tpm170) cc_final: 0.7508 (tpm170) REVERT: F 150 ASP cc_start: 0.7869 (m-30) cc_final: 0.7055 (m-30) REVERT: G 41 ASP cc_start: 0.8844 (p0) cc_final: 0.8151 (p0) REVERT: G 115 GLU cc_start: 0.7756 (mp0) cc_final: 0.7247 (mp0) REVERT: G 132 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7228 (pt0) REVERT: G 143 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: G 248 LYS cc_start: 0.8793 (mttt) cc_final: 0.8325 (mttt) REVERT: H 40 MET cc_start: 0.7350 (ttp) cc_final: 0.7102 (mtp) REVERT: H 116 MET cc_start: 0.6363 (mmt) cc_final: 0.5376 (mtm) REVERT: H 143 GLU cc_start: 0.8199 (pp20) cc_final: 0.7787 (pp20) REVERT: H 206 THR cc_start: 0.7670 (t) cc_final: 0.7410 (t) outliers start: 91 outliers final: 53 residues processed: 391 average time/residue: 0.6390 time to fit residues: 282.9983 Evaluate side-chains 377 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 309 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 221 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 154 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 75 optimal weight: 0.0060 chunk 232 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN D 117 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN G 108 GLN ** H 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117729 restraints weight = 26049.622| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.10 r_work: 0.3221 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22309 Z= 0.224 Angle : 0.624 11.807 30398 Z= 0.315 Chirality : 0.044 0.182 3536 Planarity : 0.005 0.076 3723 Dihedral : 14.361 160.766 3464 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.33 % Allowed : 18.40 % Favored : 77.27 % 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 aren not related in a simple way. whole: 0.38 (0.16), residues: 2623 helix: 1.00 (0.15), residues: 1250 sheet: -0.31 (0.21), residues: 536 loop : -0.31 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 52 TYR 0.026 0.002 TYR E 238 PHE 0.015 0.002 PHE F 169 TRP 0.008 0.001 TRP E 251 HIS 0.006 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00541 (22309) covalent geometry : angle 0.62416 (30398) hydrogen bonds : bond 0.03901 ( 1094) hydrogen bonds : angle 4.16687 ( 3123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 314 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 435 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8760 (m-30) REVERT: A 499 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7759 (mtp85) REVERT: A 546 ASP cc_start: 0.8292 (t0) cc_final: 0.7770 (t0) REVERT: A 591 GLN cc_start: 0.8303 (mt0) cc_final: 0.7994 (mp10) REVERT: A 658 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7886 (mtm-85) REVERT: A 803 TYR cc_start: 0.8420 (m-80) cc_final: 0.7937 (m-80) REVERT: A 834 LYS cc_start: 0.8201 (tttt) cc_final: 0.7992 (mppt) REVERT: A 843 LEU cc_start: 0.7956 (tp) cc_final: 0.7300 (tp) REVERT: A 847 GLU cc_start: 0.8388 (mp0) cc_final: 0.8100 (mp0) REVERT: A 855 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6839 (ttp80) REVERT: B 192 LYS cc_start: 0.8534 (mttm) cc_final: 0.8160 (ptmt) REVERT: B 264 LYS cc_start: 0.8100 (tmtp) cc_final: 0.7299 (ttmt) REVERT: B 301 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7581 (mtm110) REVERT: C 196 ASP cc_start: 0.8219 (p0) cc_final: 0.7833 (p0) REVERT: D 102 ARG cc_start: 0.8544 (ptp-170) cc_final: 0.8180 (mpp-170) REVERT: D 185 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8306 (mtt-85) REVERT: D 290 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: D 316 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: E 83 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: E 210 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7427 (tm-30) REVERT: E 231 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: E 298 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7598 (tm-30) REVERT: E 333 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8607 (tt0) REVERT: F 17 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: F 19 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7366 (pp) REVERT: F 128 ILE cc_start: 0.5739 (OUTLIER) cc_final: 0.5337 (pp) REVERT: F 146 ARG cc_start: 0.8278 (tpm170) cc_final: 0.7554 (tpm170) REVERT: F 150 ASP cc_start: 0.7869 (m-30) cc_final: 0.7022 (m-30) REVERT: G 41 ASP cc_start: 0.8856 (p0) cc_final: 0.8182 (p0) REVERT: G 115 GLU cc_start: 0.7767 (mp0) cc_final: 0.7274 (mp0) REVERT: G 132 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7201 (pt0) REVERT: G 143 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: G 248 LYS cc_start: 0.8812 (mttt) cc_final: 0.8302 (mttt) REVERT: H 1 MET cc_start: 0.6195 (ttt) cc_final: 0.5556 (tmm) REVERT: H 93 GLU cc_start: 0.6259 (mm-30) cc_final: 0.4463 (mp0) REVERT: H 116 MET cc_start: 0.6406 (mmt) cc_final: 0.5381 (mtm) REVERT: H 139 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7091 (mpp) REVERT: H 143 GLU cc_start: 0.8126 (pp20) cc_final: 0.7684 (pm20) REVERT: H 206 THR cc_start: 0.7744 (t) cc_final: 0.7483 (t) outliers start: 100 outliers final: 62 residues processed: 386 average time/residue: 0.6636 time to fit residues: 289.2376 Evaluate side-chains 382 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 304 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 763 CYS Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 855 ARG Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 65 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN D 117 GLN E 90 ASN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN G 8 GLN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 ASN ** 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 = 0.3952 r_free = 0.3952 target = 0.166250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122212 restraints weight = 25827.270| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.15 r_work: 0.3270 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22309 Z= 0.147 Angle : 0.572 12.130 30398 Z= 0.290 Chirality : 0.041 0.171 3536 Planarity : 0.004 0.074 3723 Dihedral : 14.275 160.388 3464 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.42 % Allowed : 19.65 % Favored : 76.93 % 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 aren not related in a simple way. whole: 0.57 (0.16), residues: 2623 helix: 1.18 (0.15), residues: 1251 sheet: -0.27 (0.21), residues: 537 loop : -0.21 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 52 TYR 0.027 0.001 TYR E 238 PHE 0.013 0.001 PHE A 632 TRP 0.008 0.001 TRP E 251 HIS 0.004 0.001 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00350 (22309) covalent geometry : angle 0.57246 (30398) hydrogen bonds : bond 0.03352 ( 1094) hydrogen bonds : angle 4.01502 ( 3123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 318 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8237 (tm-30) REVERT: A 435 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8504 (m-30) REVERT: A 546 ASP cc_start: 0.8328 (t0) cc_final: 0.7821 (t0) REVERT: A 591 GLN cc_start: 0.8166 (mt0) cc_final: 0.7773 (mp10) REVERT: A 658 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7805 (mtm-85) REVERT: A 803 TYR cc_start: 0.8329 (m-80) cc_final: 0.7854 (m-80) REVERT: A 834 LYS cc_start: 0.8246 (tttt) cc_final: 0.7982 (mppt) REVERT: A 843 LEU cc_start: 0.7880 (tp) cc_final: 0.7147 (tp) REVERT: A 847 GLU cc_start: 0.8397 (mp0) cc_final: 0.8121 (mp0) REVERT: B 264 LYS cc_start: 0.7935 (tmtp) cc_final: 0.7533 (tmmt) REVERT: B 301 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7408 (mtm110) REVERT: C 196 ASP cc_start: 0.8165 (p0) cc_final: 0.7815 (p0) REVERT: D 102 ARG cc_start: 0.8517 (ptp-170) cc_final: 0.8119 (mpp-170) REVERT: D 185 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8239 (mtt-85) REVERT: D 290 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7484 (mm-30) REVERT: E 27 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8183 (ttm-80) REVERT: E 143 ASP cc_start: 0.8177 (m-30) cc_final: 0.7750 (m-30) REVERT: E 210 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: E 231 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: E 298 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7571 (tm-30) REVERT: E 333 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8516 (tt0) REVERT: F 19 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7120 (pp) REVERT: F 128 ILE cc_start: 0.5808 (OUTLIER) cc_final: 0.5370 (pp) REVERT: F 146 ARG cc_start: 0.8274 (tpm170) cc_final: 0.7554 (tpm170) REVERT: F 150 ASP cc_start: 0.7858 (m-30) cc_final: 0.7016 (m-30) REVERT: G 41 ASP cc_start: 0.8770 (p0) cc_final: 0.8050 (p0) REVERT: G 116 MET cc_start: 0.8370 (mtm) cc_final: 0.8119 (mtt) REVERT: G 132 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7248 (pt0) REVERT: G 248 LYS cc_start: 0.8803 (mttt) cc_final: 0.8254 (mttt) REVERT: H 1 MET cc_start: 0.6226 (ttt) cc_final: 0.5414 (pp-130) REVERT: H 17 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: H 40 MET cc_start: 0.7126 (ttp) cc_final: 0.6871 (mtp) REVERT: H 93 GLU cc_start: 0.6240 (mm-30) cc_final: 0.4474 (mp0) REVERT: H 116 MET cc_start: 0.6390 (mmt) cc_final: 0.5382 (mtm) REVERT: H 139 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6999 (mpp) REVERT: H 143 GLU cc_start: 0.8067 (pp20) cc_final: 0.7590 (pm20) REVERT: H 206 THR cc_start: 0.7597 (t) cc_final: 0.7347 (t) outliers start: 79 outliers final: 51 residues processed: 373 average time/residue: 0.6773 time to fit residues: 285.5302 Evaluate side-chains 365 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 302 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 282 GLN Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 163 optimal weight: 0.6980 chunk 170 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN D 117 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 HIS ** H 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.166118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119713 restraints weight = 25931.905| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.10 r_work: 0.3250 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22309 Z= 0.152 Angle : 0.589 11.860 30398 Z= 0.298 Chirality : 0.041 0.164 3536 Planarity : 0.004 0.074 3723 Dihedral : 14.244 161.240 3463 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.42 % Allowed : 19.87 % Favored : 76.71 % 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 aren not related in a simple way. whole: 0.60 (0.16), residues: 2623 helix: 1.21 (0.15), residues: 1252 sheet: -0.23 (0.21), residues: 535 loop : -0.24 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 52 TYR 0.025 0.001 TYR E 238 PHE 0.014 0.001 PHE A 632 TRP 0.008 0.001 TRP E 251 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00363 (22309) covalent geometry : angle 0.58909 (30398) hydrogen bonds : bond 0.03402 ( 1094) hydrogen bonds : angle 3.98781 ( 3123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 316 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8273 (tm-30) REVERT: A 435 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8528 (m-30) REVERT: A 546 ASP cc_start: 0.8306 (t0) cc_final: 0.7847 (t0) REVERT: A 591 GLN cc_start: 0.8257 (mt0) cc_final: 0.7908 (mp10) REVERT: A 658 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7888 (mtm-85) REVERT: A 803 TYR cc_start: 0.8365 (m-80) cc_final: 0.7939 (m-80) REVERT: A 849 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7487 (tp30) REVERT: B 159 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7433 (mm-30) REVERT: B 301 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7589 (mtm110) REVERT: B 331 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8643 (m) REVERT: C 196 ASP cc_start: 0.8215 (p0) cc_final: 0.7847 (p0) REVERT: D 102 ARG cc_start: 0.8531 (ptp-170) cc_final: 0.8199 (mpp-170) REVERT: D 185 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8282 (mtt-85) REVERT: D 290 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: D 316 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7183 (mm-30) REVERT: E 143 ASP cc_start: 0.8304 (m-30) cc_final: 0.7885 (m-30) REVERT: E 210 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: E 239 PRO cc_start: 0.7386 (Cg_exo) cc_final: 0.6967 (Cg_endo) REVERT: E 298 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7657 (tm-30) REVERT: E 333 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8558 (tt0) REVERT: F 19 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7348 (pp) REVERT: F 121 LEU cc_start: 0.7145 (mt) cc_final: 0.6942 (mt) REVERT: F 128 ILE cc_start: 0.5821 (OUTLIER) cc_final: 0.5349 (pp) REVERT: F 146 ARG cc_start: 0.8267 (tpm170) cc_final: 0.7565 (tpm170) REVERT: F 150 ASP cc_start: 0.7862 (m-30) cc_final: 0.7009 (m-30) REVERT: G 41 ASP cc_start: 0.8820 (p0) cc_final: 0.8153 (p0) REVERT: G 97 ASP cc_start: 0.6810 (p0) cc_final: 0.6520 (p0) REVERT: G 132 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7272 (pt0) REVERT: G 143 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: G 248 LYS cc_start: 0.8797 (mttt) cc_final: 0.8316 (mttt) REVERT: H 1 MET cc_start: 0.6216 (ttt) cc_final: 0.5386 (pp-130) REVERT: H 40 MET cc_start: 0.7259 (ttp) cc_final: 0.7046 (mtp) REVERT: H 93 GLU cc_start: 0.6192 (mm-30) cc_final: 0.4417 (mp0) REVERT: H 116 MET cc_start: 0.6403 (mmt) cc_final: 0.5412 (mtm) REVERT: H 139 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.7070 (mmm) REVERT: H 143 GLU cc_start: 0.8103 (pp20) cc_final: 0.7670 (pm20) REVERT: H 206 THR cc_start: 0.7707 (t) cc_final: 0.7447 (t) outliers start: 79 outliers final: 51 residues processed: 377 average time/residue: 0.6618 time to fit residues: 282.3343 Evaluate side-chains 366 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 302 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 241 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN D 117 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 49 GLN F 71 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.167281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123759 restraints weight = 25934.860| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.17 r_work: 0.3287 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22309 Z= 0.126 Angle : 0.579 16.545 30398 Z= 0.291 Chirality : 0.040 0.162 3536 Planarity : 0.004 0.073 3723 Dihedral : 14.152 161.303 3462 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.81 % Allowed : 20.61 % Favored : 76.58 % 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 aren not related in a simple way. whole: 0.72 (0.17), residues: 2623 helix: 1.32 (0.15), residues: 1253 sheet: -0.23 (0.21), residues: 537 loop : -0.17 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 52 TYR 0.025 0.001 TYR E 238 PHE 0.014 0.001 PHE A 632 TRP 0.008 0.001 TRP G 28 HIS 0.003 0.000 HIS A 687 Details of bonding type rmsd covalent geometry : bond 0.00294 (22309) covalent geometry : angle 0.57880 (30398) hydrogen bonds : bond 0.03157 ( 1094) hydrogen bonds : angle 3.93066 ( 3123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 313 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 397 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: A 435 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8232 (m-30) REVERT: A 546 ASP cc_start: 0.8308 (t0) cc_final: 0.7845 (t0) REVERT: A 658 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7759 (mtm-85) REVERT: A 803 TYR cc_start: 0.8285 (m-80) cc_final: 0.7850 (m-80) REVERT: A 849 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7451 (tp30) REVERT: B 159 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7304 (mm-30) REVERT: B 301 ARG cc_start: 0.7719 (ttm-80) cc_final: 0.7408 (mtm110) REVERT: B 331 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8572 (m) REVERT: C 26 TYR cc_start: 0.9074 (m-80) cc_final: 0.8870 (m-80) REVERT: C 196 ASP cc_start: 0.8144 (p0) cc_final: 0.7774 (p0) REVERT: D 102 ARG cc_start: 0.8484 (ptp-170) cc_final: 0.8110 (mpp-170) REVERT: D 185 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8240 (mtt-85) REVERT: D 290 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: D 316 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: E 143 ASP cc_start: 0.8205 (m-30) cc_final: 0.7757 (m-30) REVERT: E 239 PRO cc_start: 0.7358 (Cg_exo) cc_final: 0.6959 (Cg_endo) REVERT: E 298 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7664 (tm-30) REVERT: E 333 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: F 19 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7103 (pp) REVERT: F 128 ILE cc_start: 0.5940 (OUTLIER) cc_final: 0.5428 (pp) REVERT: F 146 ARG cc_start: 0.8254 (tpm170) cc_final: 0.7519 (tpm170) REVERT: F 150 ASP cc_start: 0.7873 (m-30) cc_final: 0.7045 (m-30) REVERT: G 41 ASP cc_start: 0.8738 (p0) cc_final: 0.7884 (p0) REVERT: G 132 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7217 (pt0) REVERT: G 143 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: G 248 LYS cc_start: 0.8790 (mttt) cc_final: 0.8245 (mttt) REVERT: H 1 MET cc_start: 0.6401 (ttt) cc_final: 0.5352 (pp-130) REVERT: H 40 MET cc_start: 0.7064 (ttp) cc_final: 0.6849 (mtp) REVERT: H 93 GLU cc_start: 0.6222 (mm-30) cc_final: 0.4440 (mp0) REVERT: H 116 MET cc_start: 0.6484 (mmt) cc_final: 0.5387 (mtm) REVERT: H 139 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6874 (mmm) REVERT: H 143 GLU cc_start: 0.8100 (pp20) cc_final: 0.7663 (pm20) outliers start: 65 outliers final: 42 residues processed: 359 average time/residue: 0.6376 time to fit residues: 260.3873 Evaluate side-chains 357 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 302 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 297 SER Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 257 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 HIS B 332 ASN D 117 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 49 GLN F 71 ASN ** H 213 ASN ** 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 = 0.3951 r_free = 0.3951 target = 0.166251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119934 restraints weight = 25913.574| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.09 r_work: 0.3252 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22309 Z= 0.156 Angle : 0.595 14.752 30398 Z= 0.300 Chirality : 0.042 0.205 3536 Planarity : 0.004 0.074 3723 Dihedral : 14.173 162.068 3460 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.94 % Allowed : 20.65 % Favored : 76.41 % 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 aren not related in a simple way. whole: 0.68 (0.16), residues: 2623 helix: 1.27 (0.15), residues: 1254 sheet: -0.20 (0.21), residues: 535 loop : -0.17 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 52 TYR 0.022 0.001 TYR E 238 PHE 0.015 0.001 PHE A 632 TRP 0.009 0.001 TRP E 251 HIS 0.005 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00374 (22309) covalent geometry : angle 0.59527 (30398) hydrogen bonds : bond 0.03371 ( 1094) hydrogen bonds : angle 3.97777 ( 3123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8832.45 seconds wall clock time: 150 minutes 54.48 seconds (9054.48 seconds total)