Starting phenix.real_space_refine on Fri Aug 7 12:35:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umw_42386/08_2026/8umw_42386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umw_42386/08_2026/8umw_42386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8umw_42386/08_2026/8umw_42386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umw_42386/08_2026/8umw_42386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8umw_42386/08_2026/8umw_42386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umw_42386/08_2026/8umw_42386.map" } resolution = 2.93 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= 0.001 sd= 0.078 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 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.44, per 1000 atoms: 0.20 Number of scatterers: 21860 At special positions: 0 Unit cell: (118.404, 127.512, 139.104, 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: 1.63 Conformation dependent library (CDL) restraints added in 795.8 milliseconds 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: 121 helices and 14 sheets defined 51.8% alpha, 14.4% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.797A pdb=" N GLU A 293 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 294 " --> pdb=" O TYR A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 294' Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.672A pdb=" N ALA A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 440 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 498 through 503 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: 3.768A pdb=" N SER A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.691A 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: 3.552A pdb=" N ARG A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 4.118A 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 690 Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.694A pdb=" N LEU A 694 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.687A 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: 3.646A pdb=" N SER A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 Processing helix chain 'A' and resid 762 through 770 Processing helix chain 'A' and resid 782 through 799 removed outlier: 3.715A 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: 3.629A 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 117 removed outlier: 3.674A pdb=" N ARG B 117 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'B' and resid 147 through 161 removed outlier: 3.684A pdb=" N ARG B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.785A 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: 3.571A pdb=" N ARG B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.554A pdb=" N GLN B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 259 through 272 removed outlier: 4.187A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.510A pdb=" N ALA B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.854A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 removed outlier: 3.581A pdb=" N LYS B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 350 removed outlier: 3.681A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.811A 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 37 through 50 Processing helix chain 'C' and resid 66 through 78 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.502A pdb=" N MET C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 86' 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 145 removed outlier: 3.798A pdb=" N ARG C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.555A 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 192 removed outlier: 3.594A 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: 4.061A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 removed outlier: 3.533A pdb=" N ALA C 216 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.600A 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: 3.980A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.913A 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: 3.612A pdb=" N GLN C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.520A pdb=" N VAL D 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 83 through 97 removed outlier: 3.569A 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: 3.828A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 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: 3.923A 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: 3.821A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.581A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 362 removed outlier: 4.077A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 4.069A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.872A 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: 4.206A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 65 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 removed outlier: 6.812A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 117 removed outlier: 3.589A pdb=" N VAL E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 115 " --> pdb=" O MET E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 removed outlier: 3.852A pdb=" N ARG E 149 " --> pdb=" O GLN E 145 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG E 150 " --> pdb=" O HIS E 146 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.656A pdb=" N LYS E 170 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.688A 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: 3.516A pdb=" N VAL E 253 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.584A 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: 4.178A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.477A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 removed outlier: 3.653A pdb=" N ILE F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.674A pdb=" N ILE F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.740A pdb=" N SER F 222 " --> pdb=" O THR F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 81 removed outlier: 4.027A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.740A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) 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 11 through 16 Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 82 removed outlier: 3.686A pdb=" N LYS H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA H 82 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 190 through 194 removed outlier: 3.877A pdb=" N GLU H 193 " --> pdb=" O LYS H 190 " (cutoff:3.500A) removed outlier: 3.975A 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: 6.107A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET A 398 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 370 " --> pdb=" O CYS A 488 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N CYS A 490 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 372 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A 369 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU A 508 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU A 371 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 803 through 806 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.082A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.238A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.384A 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: 6.350A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.016A 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: 6.914A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N HIS E 37 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL E 182 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 62 removed outlier: 3.736A pdb=" N VAL G 167 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 71 removed outlier: 7.149A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 177 through 179 removed outlier: 4.759A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 61 through 62 removed outlier: 4.663A pdb=" N VAL G 111 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS H 181 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.652A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 61 Processing sheet with id=AB5, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.704A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR H 196 " --> pdb=" O LYS H 138 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 3126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 4.02 Time building geometry restraints manager: 2.37 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: 7236 1.36 - 1.50: 5710 1.50 - 1.65: 9155 1.65 - 1.80: 103 1.80 - 1.95: 105 Bond restraints: 22309 Sorted by residual: bond pdb=" C HIS B 259 " pdb=" N PRO B 260 " ideal model delta sigma weight residual 1.336 1.398 -0.062 1.25e-02 6.40e+03 2.50e+01 bond pdb=" O2G AGS C 402 " pdb=" PG AGS C 402 " ideal model delta sigma weight residual 1.604 1.507 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" O3B AGS A1202 " pdb=" PB AGS A1202 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" O3B AGS B 402 " pdb=" PB AGS B 402 " ideal model delta sigma weight residual 1.673 1.586 0.087 2.00e-02 2.50e+03 1.87e+01 ... (remaining 22304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 29684 2.20 - 4.40: 616 4.40 - 6.59: 71 6.59 - 8.79: 23 8.79 - 10.99: 4 Bond angle restraints: 30398 Sorted by residual: angle pdb=" C MET C 182 " pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 120.33 124.42 -4.09 8.00e-01 1.56e+00 2.61e+01 angle pdb=" C PRO B 258 " pdb=" N HIS B 259 " pdb=" CA HIS B 259 " ideal model delta sigma weight residual 120.26 126.94 -6.68 1.34e+00 5.57e-01 2.49e+01 angle pdb=" N3 DT I 13 " pdb=" C4 DT I 13 " pdb=" O4 DT I 13 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" O LYS G 181 " pdb=" C LYS G 181 " pdb=" N LEU G 182 " ideal model delta sigma weight residual 123.31 128.45 -5.14 1.17e+00 7.31e-01 1.93e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.53: 13219 34.53 - 69.07: 454 69.07 - 103.60: 23 103.60 - 138.13: 6 138.13 - 172.67: 5 Dihedral angle restraints: 13707 sinusoidal: 5967 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 300.00 157.72 142.28 1 2.00e+01 2.50e-03 4.30e+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 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA LEU F 79 " pdb=" C LEU F 79 " pdb=" N LYS F 80 " pdb=" CA LYS F 80 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 13704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3087 0.069 - 0.137: 404 0.137 - 0.206: 30 0.206 - 0.274: 4 0.274 - 0.343: 3 Chirality restraints: 3528 Sorted by residual: chirality pdb=" CA LEU G 182 " pdb=" N LEU G 182 " pdb=" C LEU G 182 " pdb=" CB LEU G 182 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C3' AGS D 402 " pdb=" C2' AGS D 402 " pdb=" C4' AGS D 402 " pdb=" O3' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C3' AGS B 402 " pdb=" C2' AGS B 402 " pdb=" C4' AGS B 402 " pdb=" O3' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 3525 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " 0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO A 699 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 173 " -0.047 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO E 174 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 160 " -0.233 9.50e-02 1.11e+02 1.04e-01 6.69e+00 pdb=" NE ARG E 160 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG E 160 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG E 160 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 160 " -0.008 2.00e-02 2.50e+03 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 223 2.62 - 3.19: 17235 3.19 - 3.76: 34257 3.76 - 4.33: 47702 4.33 - 4.90: 79243 Nonbonded interactions: 178660 Sorted by model distance: nonbonded pdb=" OG1 THR D 85 " pdb="MG MG D 401 " model vdw 2.045 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.045 2.170 nonbonded pdb=" OG1 THR C 67 " pdb="MG MG C 401 " model vdw 2.058 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.058 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2G AGS B 402 " model vdw 2.062 2.170 ... (remaining 178655 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.410 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 22309 Z= 0.285 Angle : 0.742 10.992 30398 Z= 0.456 Chirality : 0.047 0.343 3528 Planarity : 0.007 0.104 3723 Dihedral : 15.976 172.666 8669 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.90 % Allowed : 8.83 % Favored : 89.26 % 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 are not related in a simple way. whole: -1.73 (0.14), residues: 2623 helix: -1.36 (0.12), residues: 1250 sheet: -0.23 (0.23), residues: 512 loop : -1.04 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.015 0.002 TYR D 77 PHE 0.019 0.002 PHE A 632 TRP 0.008 0.001 TRP E 251 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.28 (22309) covalent geometry : angle 0.74226 / 0.46 (30398) hydrogen bonds : bond 0.14113 / 9.56 ( 1124) hydrogen bonds : angle 5.86761 / 4.16 ( 3210) *********************** 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 558 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 514 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 531 MET cc_start: 0.6518 (mmt) cc_final: 0.6039 (mmt) REVERT: A 767 ASP cc_start: 0.7412 (t70) cc_final: 0.7181 (t0) REVERT: C 89 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7371 (tm-30) REVERT: C 307 ASP cc_start: 0.8311 (m-30) cc_final: 0.8033 (m-30) REVERT: D 209 GLN cc_start: 0.8151 (tt0) cc_final: 0.7922 (mt0) REVERT: D 221 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8303 (mttt) REVERT: E 11 CYS cc_start: 0.7786 (m) cc_final: 0.7571 (p) REVERT: E 191 ASP cc_start: 0.7367 (m-30) cc_final: 0.7157 (m-30) REVERT: F 71 ASN cc_start: 0.8259 (t0) cc_final: 0.7958 (t0) REVERT: F 114 TYR cc_start: 0.0312 (m-80) cc_final: 0.0058 (m-80) REVERT: F 240 LYS cc_start: 0.8005 (tppp) cc_final: 0.7802 (mtmp) REVERT: F 248 LYS cc_start: 0.8313 (mttt) cc_final: 0.7597 (mtpt) REVERT: G 147 ILE cc_start: 0.8716 (tt) cc_final: 0.8339 (mt) REVERT: G 222 SER cc_start: 0.8099 (m) cc_final: 0.7647 (t) REVERT: H 160 ILE cc_start: 0.8901 (mm) cc_final: 0.8694 (mm) REVERT: H 196 THR cc_start: 0.8618 (p) cc_final: 0.8360 (t) REVERT: H 214 PHE cc_start: 0.8507 (m-10) cc_final: 0.8118 (m-80) REVERT: H 219 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.6929 (t) REVERT: H 230 SER cc_start: 0.8621 (t) cc_final: 0.8398 (m) outliers start: 44 outliers final: 14 residues processed: 538 average time/residue: 0.5136 time to fit residues: 314.4764 Evaluate side-chains 334 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 319 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 HIS A 723 GLN A 724 GLN A 727 GLN A 732 GLN A 755 GLN B 125 GLN B 226 GLN B 268 GLN B 269 HIS ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN C 29 GLN C 37 HIS C 257 GLN C 317 ASN C 330 GLN D 357 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 194 HIS F 8 GLN F 44 HIS G 108 GLN H 36 ASN H 38 GLN H 44 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123111 restraints weight = 27079.196| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.05 r_work: 0.3318 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22309 Z= 0.194 Angle : 0.623 12.789 30398 Z= 0.323 Chirality : 0.043 0.169 3528 Planarity : 0.005 0.082 3723 Dihedral : 16.564 173.491 3552 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.03 % Allowed : 15.67 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2623 helix: 0.13 (0.14), residues: 1261 sheet: -0.39 (0.22), residues: 516 loop : -0.61 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 93 TYR 0.014 0.002 TYR H 133 PHE 0.019 0.002 PHE F 144 TRP 0.006 0.001 TRP E 251 HIS 0.010 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (22309) covalent geometry : angle 0.62292 / 0.32 (30398) hydrogen bonds : bond 0.04085 / 2.74 ( 1124) hydrogen bonds : angle 4.39204 / 3.14 ( 3210) *********************** 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 430 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 337 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 354 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7226 (ttm) REVERT: A 531 MET cc_start: 0.6250 (mmt) cc_final: 0.5963 (mmt) REVERT: A 560 TYR cc_start: 0.8255 (m-80) cc_final: 0.7567 (m-80) REVERT: A 767 ASP cc_start: 0.7770 (t70) cc_final: 0.7538 (t0) REVERT: A 853 MET cc_start: 0.7510 (ppp) cc_final: 0.6639 (mmm) REVERT: B 207 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: B 336 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: B 348 THR cc_start: 0.9144 (m) cc_final: 0.8631 (p) REVERT: C 50 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: C 86 MET cc_start: 0.9145 (mmm) cc_final: 0.8766 (mmm) REVERT: C 130 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8704 (mtp) REVERT: C 307 ASP cc_start: 0.8468 (m-30) cc_final: 0.8210 (m-30) REVERT: D 172 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8039 (mttm) REVERT: D 209 GLN cc_start: 0.8457 (tt0) cc_final: 0.7898 (mt0) REVERT: D 290 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: E 11 CYS cc_start: 0.8181 (m) cc_final: 0.7753 (p) REVERT: E 83 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7139 (tp30) REVERT: E 111 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8472 (ttt) REVERT: E 298 GLU cc_start: 0.8247 (tp30) cc_final: 0.8008 (tp30) REVERT: F 1 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7137 (tpt) REVERT: F 17 GLU cc_start: 0.7800 (tp30) cc_final: 0.7542 (tp30) REVERT: F 21 ASP cc_start: 0.7679 (t70) cc_final: 0.7429 (t0) REVERT: F 53 ARG cc_start: 0.8390 (mpp80) cc_final: 0.8184 (mpp80) REVERT: F 64 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7832 (mtm110) REVERT: F 71 ASN cc_start: 0.8398 (t0) cc_final: 0.7944 (t0) REVERT: F 72 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8303 (tm) REVERT: F 87 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7050 (tt) REVERT: F 240 LYS cc_start: 0.8496 (tppp) cc_final: 0.7899 (mtmp) REVERT: F 248 LYS cc_start: 0.8718 (mttt) cc_final: 0.7668 (mtpt) REVERT: G 49 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: G 61 ARG cc_start: 0.8138 (ptt180) cc_final: 0.7679 (ptt-90) REVERT: G 77 LYS cc_start: 0.8533 (ptpt) cc_final: 0.8216 (ptpt) REVERT: G 147 ILE cc_start: 0.8709 (tt) cc_final: 0.8409 (mt) REVERT: G 199 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6311 (mpt) REVERT: G 222 SER cc_start: 0.8317 (m) cc_final: 0.7800 (t) REVERT: G 240 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7816 (tptp) REVERT: G 250 TYR cc_start: 0.9016 (m-80) cc_final: 0.7875 (m-80) REVERT: H 98 THR cc_start: 0.6202 (OUTLIER) cc_final: 0.5892 (m) REVERT: H 162 CYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7446 (t) REVERT: H 196 THR cc_start: 0.8665 (p) cc_final: 0.8436 (t) REVERT: H 219 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7209 (t) REVERT: H 230 SER cc_start: 0.8869 (t) cc_final: 0.8566 (m) outliers start: 93 outliers final: 36 residues processed: 393 average time/residue: 0.5053 time to fit residues: 227.5798 Evaluate side-chains 353 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 30 ILE 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 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 26 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 194 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 252 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 29 GLN C 37 HIS ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 194 HIS F 8 GLN F 184 GLN H 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.162864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125113 restraints weight = 27193.320| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.06 r_work: 0.3309 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 22309 Z= 0.169 Angle : 0.571 10.872 30398 Z= 0.296 Chirality : 0.041 0.167 3528 Planarity : 0.004 0.076 3723 Dihedral : 16.245 173.894 3539 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.98 % Allowed : 17.01 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 2623 helix: 0.68 (0.14), residues: 1263 sheet: -0.33 (0.22), residues: 511 loop : -0.45 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 264 TYR 0.019 0.002 TYR H 133 PHE 0.014 0.001 PHE H 144 TRP 0.009 0.001 TRP E 251 HIS 0.007 0.001 HIS E 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (22309) covalent geometry : angle 0.57100 / 0.30 (30398) hydrogen bonds : bond 0.03675 / 2.46 ( 1124) hydrogen bonds : angle 4.20067 / 3.01 ( 3210) *********************** 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 410 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 318 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 354 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7293 (ttm) REVERT: A 387 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 531 MET cc_start: 0.6385 (mmt) cc_final: 0.6075 (mmt) REVERT: A 560 TYR cc_start: 0.8247 (m-80) cc_final: 0.7669 (m-80) REVERT: A 822 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7427 (pp20) REVERT: A 853 MET cc_start: 0.7548 (ppp) cc_final: 0.6706 (mmm) REVERT: B 207 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: B 336 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8212 (mp10) REVERT: B 348 THR cc_start: 0.9113 (m) cc_final: 0.8649 (p) REVERT: C 50 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: C 86 MET cc_start: 0.9077 (mmm) cc_final: 0.8738 (mmm) REVERT: C 130 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8727 (mtp) REVERT: C 307 ASP cc_start: 0.8507 (m-30) cc_final: 0.8258 (m-30) REVERT: D 209 GLN cc_start: 0.8487 (tt0) cc_final: 0.7951 (mt0) REVERT: D 290 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: E 11 CYS cc_start: 0.8105 (m) cc_final: 0.7745 (p) REVERT: E 83 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7056 (tp30) REVERT: E 139 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8467 (mtpt) REVERT: E 298 GLU cc_start: 0.8282 (tp30) cc_final: 0.8070 (tp30) REVERT: F 17 GLU cc_start: 0.7804 (tp30) cc_final: 0.7270 (tp30) REVERT: F 21 ASP cc_start: 0.7894 (t70) cc_final: 0.7564 (t0) REVERT: F 64 ARG cc_start: 0.8201 (mtm110) cc_final: 0.7911 (mtm110) REVERT: F 71 ASN cc_start: 0.8612 (t0) cc_final: 0.8385 (t0) REVERT: F 72 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8410 (tm) REVERT: F 87 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7181 (pp) REVERT: F 115 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7559 (mt-10) REVERT: F 240 LYS cc_start: 0.8534 (tppp) cc_final: 0.7945 (mtmp) REVERT: F 248 LYS cc_start: 0.8738 (mttt) cc_final: 0.7694 (mtpt) REVERT: G 61 ARG cc_start: 0.8233 (ptt180) cc_final: 0.7778 (ptt-90) REVERT: G 77 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8264 (ptpt) REVERT: G 147 ILE cc_start: 0.8723 (tt) cc_final: 0.8414 (mt) REVERT: G 199 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6529 (mpt) REVERT: G 222 SER cc_start: 0.8296 (m) cc_final: 0.7861 (t) REVERT: G 240 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7874 (tptp) REVERT: G 250 TYR cc_start: 0.8992 (m-80) cc_final: 0.7891 (m-80) REVERT: H 75 MET cc_start: 0.7366 (ttt) cc_final: 0.7108 (ttt) REVERT: H 196 THR cc_start: 0.8643 (p) cc_final: 0.8411 (t) REVERT: H 219 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7240 (t) REVERT: H 230 SER cc_start: 0.8866 (t) cc_final: 0.8570 (m) outliers start: 92 outliers final: 36 residues processed: 376 average time/residue: 0.4874 time to fit residues: 211.0985 Evaluate side-chains 343 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 114 optimal weight: 3.9990 chunk 246 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 172 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 HIS C 37 HIS C 317 ASN E 120 GLN E 124 ASN F 8 GLN F 36 ASN F 213 ASN H 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.163434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125212 restraints weight = 27107.203| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.08 r_work: 0.3326 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22309 Z= 0.114 Angle : 0.531 8.068 30398 Z= 0.276 Chirality : 0.040 0.174 3528 Planarity : 0.004 0.073 3723 Dihedral : 16.041 173.121 3533 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.16 % Allowed : 17.53 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2623 helix: 1.02 (0.15), residues: 1261 sheet: -0.32 (0.22), residues: 513 loop : -0.30 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 65 TYR 0.013 0.001 TYR A 633 PHE 0.012 0.001 PHE A 692 TRP 0.008 0.001 TRP E 251 HIS 0.004 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (22309) covalent geometry : angle 0.53119 / 0.28 (30398) hydrogen bonds : bond 0.03215 / 2.15 ( 1124) hydrogen bonds : angle 4.04273 / 2.89 ( 3210) *********************** 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 416 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 320 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 354 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7223 (ttp) REVERT: A 387 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 531 MET cc_start: 0.6379 (mmt) cc_final: 0.6042 (mmt) REVERT: A 560 TYR cc_start: 0.8251 (m-80) cc_final: 0.7662 (m-80) REVERT: A 740 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7939 (tp) REVERT: A 822 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7468 (pp20) REVERT: A 853 MET cc_start: 0.7534 (ppp) cc_final: 0.6741 (mmm) REVERT: B 336 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8188 (mp10) REVERT: B 348 THR cc_start: 0.9102 (m) cc_final: 0.8636 (p) REVERT: C 50 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: C 86 MET cc_start: 0.9070 (mmm) cc_final: 0.8746 (mmm) REVERT: C 130 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8734 (mtp) REVERT: C 307 ASP cc_start: 0.8486 (m-30) cc_final: 0.8236 (m-30) REVERT: D 209 GLN cc_start: 0.8487 (tt0) cc_final: 0.7969 (mt0) REVERT: D 290 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: D 299 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: E 11 CYS cc_start: 0.8101 (m) cc_final: 0.7736 (p) REVERT: E 139 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8470 (mtpt) REVERT: E 298 GLU cc_start: 0.8271 (tp30) cc_final: 0.8061 (tp30) REVERT: F 1 MET cc_start: 0.7736 (tpp) cc_final: 0.7332 (tpt) REVERT: F 17 GLU cc_start: 0.7776 (tp30) cc_final: 0.7233 (tp30) REVERT: F 21 ASP cc_start: 0.7898 (t70) cc_final: 0.7446 (t0) REVERT: F 53 ARG cc_start: 0.8385 (mpp80) cc_final: 0.8057 (mpp80) REVERT: F 64 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7999 (mtm110) REVERT: F 71 ASN cc_start: 0.8562 (t0) cc_final: 0.8342 (t0) REVERT: F 72 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8380 (tm) REVERT: F 87 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7134 (pp) REVERT: F 115 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7516 (mt-10) REVERT: F 240 LYS cc_start: 0.8558 (tppp) cc_final: 0.7948 (mtmp) REVERT: F 248 LYS cc_start: 0.8756 (mttt) cc_final: 0.7743 (mtpt) REVERT: G 61 ARG cc_start: 0.8217 (ptt180) cc_final: 0.7824 (ptt-90) REVERT: G 77 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8179 (ptpt) REVERT: G 103 PHE cc_start: 0.8159 (p90) cc_final: 0.7927 (p90) REVERT: G 116 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7970 (mmm) REVERT: G 147 ILE cc_start: 0.8681 (tt) cc_final: 0.8375 (mt) REVERT: G 222 SER cc_start: 0.8274 (m) cc_final: 0.7856 (t) REVERT: G 240 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7864 (tptp) REVERT: G 250 TYR cc_start: 0.8994 (m-80) cc_final: 0.7920 (m-80) REVERT: H 162 CYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7293 (t) REVERT: H 196 THR cc_start: 0.8653 (p) cc_final: 0.8402 (t) REVERT: H 219 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7140 (t) REVERT: H 230 SER cc_start: 0.8807 (t) cc_final: 0.8525 (m) outliers start: 96 outliers final: 37 residues processed: 377 average time/residue: 0.5169 time to fit residues: 224.1924 Evaluate side-chains 351 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 60 optimal weight: 0.0770 chunk 87 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 238 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 243 optimal weight: 0.0050 chunk 17 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 132 optimal weight: 0.0870 chunk 197 optimal weight: 9.9990 overall best weight: 0.3130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 HIS C 37 HIS C 257 GLN C 317 ASN E 124 ASN F 8 GLN F 36 ASN F 213 ASN H 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.164066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.128934 restraints weight = 26846.000| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.91 r_work: 0.3397 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22309 Z= 0.102 Angle : 0.509 8.141 30398 Z= 0.266 Chirality : 0.039 0.156 3528 Planarity : 0.004 0.072 3723 Dihedral : 15.894 172.915 3533 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.77 % Allowed : 18.83 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2623 helix: 1.23 (0.15), residues: 1264 sheet: -0.19 (0.22), residues: 505 loop : -0.24 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 264 TYR 0.016 0.001 TYR H 133 PHE 0.023 0.001 PHE F 144 TRP 0.008 0.001 TRP E 251 HIS 0.004 0.000 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (22309) covalent geometry : angle 0.50926 / 0.27 (30398) hydrogen bonds : bond 0.03025 / 2.02 ( 1124) hydrogen bonds : angle 3.94162 / 2.81 ( 3210) *********************** 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 407 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 320 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 354 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7298 (ttp) REVERT: A 387 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8037 (mp) REVERT: A 531 MET cc_start: 0.6427 (mmt) cc_final: 0.6164 (mmt) REVERT: A 560 TYR cc_start: 0.8204 (m-80) cc_final: 0.7702 (m-80) REVERT: A 740 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7925 (tp) REVERT: A 822 GLU cc_start: 0.7765 (pt0) cc_final: 0.7483 (pp20) REVERT: A 852 LYS cc_start: 0.7920 (tppt) cc_final: 0.7487 (tttt) REVERT: A 853 MET cc_start: 0.7443 (ppp) cc_final: 0.6698 (mmm) REVERT: B 348 THR cc_start: 0.9086 (m) cc_final: 0.8638 (p) REVERT: C 50 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: C 86 MET cc_start: 0.9030 (mmm) cc_final: 0.8720 (mmm) REVERT: C 307 ASP cc_start: 0.8413 (m-30) cc_final: 0.8174 (m-30) REVERT: D 209 GLN cc_start: 0.8432 (tt0) cc_final: 0.7958 (mt0) REVERT: D 290 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: D 299 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8193 (mm-30) REVERT: E 11 CYS cc_start: 0.8067 (m) cc_final: 0.7719 (p) REVERT: E 83 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: E 139 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8474 (mtpt) REVERT: E 160 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8606 (tpp-160) REVERT: E 298 GLU cc_start: 0.8238 (tp30) cc_final: 0.7980 (tp30) REVERT: F 1 MET cc_start: 0.7796 (tpp) cc_final: 0.7373 (tpt) REVERT: F 17 GLU cc_start: 0.7715 (tp30) cc_final: 0.7155 (tp30) REVERT: F 21 ASP cc_start: 0.7728 (t70) cc_final: 0.7260 (t0) REVERT: F 71 ASN cc_start: 0.8521 (t0) cc_final: 0.8282 (t0) REVERT: F 72 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8350 (tm) REVERT: F 87 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7020 (tt) REVERT: F 115 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7506 (mt-10) REVERT: F 144 PHE cc_start: 0.8554 (t80) cc_final: 0.8227 (t80) REVERT: F 240 LYS cc_start: 0.8527 (tppp) cc_final: 0.7934 (mtmp) REVERT: F 248 LYS cc_start: 0.8712 (mttt) cc_final: 0.7699 (mtpt) REVERT: G 61 ARG cc_start: 0.8182 (ptt180) cc_final: 0.7730 (ptt-90) REVERT: G 77 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8108 (ptpt) REVERT: G 91 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7988 (mtm-85) REVERT: G 103 PHE cc_start: 0.8193 (p90) cc_final: 0.7959 (p90) REVERT: G 116 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8060 (mmm) REVERT: G 147 ILE cc_start: 0.8652 (tt) cc_final: 0.8352 (mt) REVERT: G 222 SER cc_start: 0.8256 (m) cc_final: 0.7848 (t) REVERT: G 250 TYR cc_start: 0.8965 (m-80) cc_final: 0.7914 (m-80) REVERT: H 16 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8582 (tm) REVERT: H 75 MET cc_start: 0.7415 (ttt) cc_final: 0.7136 (ttt) REVERT: H 133 TYR cc_start: 0.7792 (m-80) cc_final: 0.7589 (m-80) REVERT: H 162 CYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7289 (t) REVERT: H 196 THR cc_start: 0.8662 (p) cc_final: 0.8406 (t) REVERT: H 219 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7219 (t) REVERT: H 230 SER cc_start: 0.8809 (t) cc_final: 0.8545 (m) outliers start: 87 outliers final: 38 residues processed: 373 average time/residue: 0.4897 time to fit residues: 209.0468 Evaluate side-chains 354 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain F residue 11 ILE 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 75 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 208 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 117 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 29 GLN C 37 HIS C 317 ASN C 330 GLN E 124 ASN F 8 GLN F 36 ASN F 213 ASN H 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.161281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126176 restraints weight = 26918.100| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.83 r_work: 0.3380 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22309 Z= 0.128 Angle : 0.528 9.503 30398 Z= 0.273 Chirality : 0.040 0.174 3528 Planarity : 0.004 0.071 3723 Dihedral : 15.832 170.937 3533 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.03 % Allowed : 19.22 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2623 helix: 1.28 (0.15), residues: 1265 sheet: -0.21 (0.22), residues: 508 loop : -0.19 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 264 TYR 0.012 0.001 TYR A 291 PHE 0.016 0.001 PHE F 144 TRP 0.009 0.001 TRP H 28 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (22309) covalent geometry : angle 0.52754 / 0.27 (30398) hydrogen bonds : bond 0.03122 / 2.10 ( 1124) hydrogen bonds : angle 3.90788 / 2.79 ( 3210) *********************** 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 407 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 314 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8052 (tm-30) REVERT: A 354 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7330 (ttp) REVERT: A 387 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8052 (mp) REVERT: A 531 MET cc_start: 0.6442 (mmt) cc_final: 0.6073 (mmt) REVERT: A 560 TYR cc_start: 0.8204 (m-80) cc_final: 0.7740 (m-80) REVERT: A 740 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7967 (tp) REVERT: A 806 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6127 (mt-10) REVERT: A 822 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7545 (pp20) REVERT: A 853 MET cc_start: 0.7404 (ppp) cc_final: 0.6677 (mmm) REVERT: B 114 ASP cc_start: 0.8395 (m-30) cc_final: 0.8188 (m-30) REVERT: B 336 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8145 (mp10) REVERT: B 348 THR cc_start: 0.9077 (m) cc_final: 0.8625 (p) REVERT: C 50 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: C 86 MET cc_start: 0.9015 (mmm) cc_final: 0.8756 (mmm) REVERT: C 130 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8740 (mtp) REVERT: C 307 ASP cc_start: 0.8421 (m-30) cc_final: 0.8185 (m-30) REVERT: D 209 GLN cc_start: 0.8436 (tt0) cc_final: 0.7956 (mt0) REVERT: D 290 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7353 (mt-10) REVERT: D 299 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8181 (mm-30) REVERT: D 316 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5170 (mp0) REVERT: E 11 CYS cc_start: 0.8078 (m) cc_final: 0.7733 (p) REVERT: E 83 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6933 (tp30) REVERT: E 139 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8516 (mtpt) REVERT: F 1 MET cc_start: 0.7825 (tpp) cc_final: 0.7418 (tpt) REVERT: F 17 GLU cc_start: 0.7743 (tp30) cc_final: 0.7185 (tp30) REVERT: F 21 ASP cc_start: 0.7723 (t70) cc_final: 0.7264 (t0) REVERT: F 64 ARG cc_start: 0.8225 (mtm110) cc_final: 0.7989 (mtm110) REVERT: F 71 ASN cc_start: 0.8582 (t0) cc_final: 0.8351 (t0) REVERT: F 72 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8479 (tm) REVERT: F 87 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7161 (pp) REVERT: F 115 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7550 (mt-10) REVERT: F 144 PHE cc_start: 0.8564 (t80) cc_final: 0.8326 (t80) REVERT: F 168 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6490 (mmtm) REVERT: F 214 PHE cc_start: 0.8625 (m-10) cc_final: 0.8349 (m-10) REVERT: F 240 LYS cc_start: 0.8576 (tppp) cc_final: 0.8033 (mtmp) REVERT: F 248 LYS cc_start: 0.8729 (mttt) cc_final: 0.7721 (mtpt) REVERT: G 61 ARG cc_start: 0.8203 (ptt180) cc_final: 0.7815 (ptt-90) REVERT: G 77 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8142 (ptpt) REVERT: G 116 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7879 (mmm) REVERT: G 147 ILE cc_start: 0.8696 (tt) cc_final: 0.8404 (mt) REVERT: G 222 SER cc_start: 0.8256 (m) cc_final: 0.7863 (t) REVERT: G 250 TYR cc_start: 0.8967 (m-80) cc_final: 0.7933 (m-80) REVERT: H 16 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8538 (tm) REVERT: H 75 MET cc_start: 0.7415 (ttt) cc_final: 0.7076 (ttt) REVERT: H 162 CYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7237 (t) REVERT: H 196 THR cc_start: 0.8676 (p) cc_final: 0.8426 (t) REVERT: H 219 THR cc_start: 0.7516 (OUTLIER) cc_final: 0.7253 (t) REVERT: H 230 SER cc_start: 0.8822 (t) cc_final: 0.8573 (m) outliers start: 93 outliers final: 47 residues processed: 372 average time/residue: 0.5153 time to fit residues: 221.1763 Evaluate side-chains 364 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 297 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 221 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 179 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 255 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 37 HIS C 317 ASN F 8 GLN F 36 ASN F 213 ASN H 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.159903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124763 restraints weight = 26963.623| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.83 r_work: 0.3361 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22309 Z= 0.158 Angle : 0.552 10.117 30398 Z= 0.284 Chirality : 0.041 0.160 3528 Planarity : 0.004 0.071 3723 Dihedral : 15.849 167.707 3533 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.33 % Allowed : 19.74 % Favored : 75.93 % 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 are not related in a simple way. whole: 0.67 (0.17), residues: 2623 helix: 1.30 (0.15), residues: 1263 sheet: -0.32 (0.22), residues: 517 loop : -0.18 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 264 TYR 0.013 0.001 TYR A 291 PHE 0.013 0.001 PHE F 57 TRP 0.010 0.001 TRP H 28 HIS 0.005 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (22309) covalent geometry : angle 0.55208 / 0.28 (30398) hydrogen bonds : bond 0.03297 / 2.22 ( 1124) hydrogen bonds : angle 3.93031 / 2.81 ( 3210) *********************** 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 415 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 315 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 354 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7358 (ttp) REVERT: A 387 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8088 (mp) REVERT: A 531 MET cc_start: 0.6505 (mmt) cc_final: 0.6172 (mmt) REVERT: A 541 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8058 (tt) REVERT: A 560 TYR cc_start: 0.8216 (m-80) cc_final: 0.7800 (m-80) REVERT: A 740 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8020 (tp) REVERT: A 758 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8201 (tp) REVERT: A 806 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6134 (mt-10) REVERT: A 822 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7581 (pp20) REVERT: A 847 GLU cc_start: 0.8640 (mm-30) cc_final: 0.7767 (tt0) REVERT: A 852 LYS cc_start: 0.7926 (tppt) cc_final: 0.7494 (tttt) REVERT: A 853 MET cc_start: 0.7386 (ppp) cc_final: 0.6648 (mmm) REVERT: B 114 ASP cc_start: 0.8396 (m-30) cc_final: 0.8185 (m-30) REVERT: B 336 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8162 (mp10) REVERT: B 348 THR cc_start: 0.9071 (m) cc_final: 0.8608 (p) REVERT: C 50 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: C 86 MET cc_start: 0.8996 (mmm) cc_final: 0.8762 (mmm) REVERT: C 130 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8737 (mtp) REVERT: C 307 ASP cc_start: 0.8448 (m-30) cc_final: 0.8209 (m-30) REVERT: D 209 GLN cc_start: 0.8450 (tt0) cc_final: 0.7973 (mt0) REVERT: D 290 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: D 316 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5136 (mp0) REVERT: E 11 CYS cc_start: 0.8054 (m) cc_final: 0.7714 (p) REVERT: E 83 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6983 (tp30) REVERT: E 139 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8529 (mtpt) REVERT: E 160 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8645 (tpp-160) REVERT: F 1 MET cc_start: 0.7841 (tpp) cc_final: 0.7436 (tpt) REVERT: F 17 GLU cc_start: 0.7828 (tp30) cc_final: 0.7278 (tp30) REVERT: F 21 ASP cc_start: 0.7785 (t70) cc_final: 0.7324 (t0) REVERT: F 71 ASN cc_start: 0.8587 (t0) cc_final: 0.8352 (t0) REVERT: F 72 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8430 (tm) REVERT: F 87 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7165 (pp) REVERT: F 115 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7581 (mt-10) REVERT: F 168 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6492 (mmtm) REVERT: F 240 LYS cc_start: 0.8577 (tppp) cc_final: 0.7992 (mtmp) REVERT: F 248 LYS cc_start: 0.8739 (mttt) cc_final: 0.7729 (mtpt) REVERT: G 61 ARG cc_start: 0.8205 (ptt180) cc_final: 0.7804 (ptt-90) REVERT: G 77 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8296 (ptpt) REVERT: G 80 LYS cc_start: 0.7782 (mtpt) cc_final: 0.7441 (tptm) REVERT: G 116 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7862 (mmm) REVERT: G 132 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7201 (pp20) REVERT: G 147 ILE cc_start: 0.8738 (tt) cc_final: 0.8442 (mt) REVERT: G 222 SER cc_start: 0.8287 (m) cc_final: 0.7891 (t) REVERT: G 250 TYR cc_start: 0.8973 (m-80) cc_final: 0.7867 (m-80) REVERT: H 16 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8520 (tm) REVERT: H 75 MET cc_start: 0.7424 (ttt) cc_final: 0.7083 (ttt) REVERT: H 162 CYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7315 (t) REVERT: H 196 THR cc_start: 0.8691 (p) cc_final: 0.8447 (t) REVERT: H 219 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7329 (t) REVERT: H 230 SER cc_start: 0.8849 (t) cc_final: 0.8612 (m) outliers start: 100 outliers final: 50 residues processed: 377 average time/residue: 0.5368 time to fit residues: 233.3374 Evaluate side-chains 371 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 298 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 65 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 37 HIS C 285 HIS C 317 ASN F 8 GLN F 36 ASN F 38 GLN F 213 ASN H 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.157573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117844 restraints weight = 27026.214| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.45 r_work: 0.3235 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 22309 Z= 0.255 Angle : 0.651 9.773 30398 Z= 0.332 Chirality : 0.045 0.171 3528 Planarity : 0.005 0.073 3723 Dihedral : 16.039 171.036 3533 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.59 % Allowed : 19.91 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2623 helix: 1.01 (0.15), residues: 1272 sheet: -0.54 (0.22), residues: 511 loop : -0.30 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 264 TYR 0.022 0.002 TYR H 133 PHE 0.014 0.002 PHE E 339 TRP 0.013 0.002 TRP H 28 HIS 0.007 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.25 (22309) covalent geometry : angle 0.65071 / 0.33 (30398) hydrogen bonds : bond 0.04095 / 2.77 ( 1124) hydrogen bonds : angle 4.20326 / 3.03 ( 3210) *********************** 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 408 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 302 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 354 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7226 (ttp) REVERT: A 387 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 531 MET cc_start: 0.6379 (mmt) cc_final: 0.5877 (mmt) REVERT: A 560 TYR cc_start: 0.8280 (m-80) cc_final: 0.7788 (m-80) REVERT: A 740 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7918 (tp) REVERT: A 758 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8183 (tp) REVERT: A 853 MET cc_start: 0.7373 (ppp) cc_final: 0.6621 (mmm) REVERT: B 336 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: C 50 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: C 130 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8783 (mtp) REVERT: C 307 ASP cc_start: 0.8502 (m-30) cc_final: 0.8280 (m-30) REVERT: D 209 GLN cc_start: 0.8505 (tt0) cc_final: 0.7956 (mt0) REVERT: D 290 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: D 316 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5290 (mp0) REVERT: E 11 CYS cc_start: 0.8231 (m) cc_final: 0.7912 (p) REVERT: E 83 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6956 (tp30) REVERT: E 111 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8505 (ttt) REVERT: E 139 LYS cc_start: 0.8898 (mtpp) cc_final: 0.8470 (mtpt) REVERT: F 1 MET cc_start: 0.7806 (tpp) cc_final: 0.7394 (tpt) REVERT: F 17 GLU cc_start: 0.7901 (tp30) cc_final: 0.7352 (tp30) REVERT: F 21 ASP cc_start: 0.7838 (t70) cc_final: 0.7387 (t0) REVERT: F 64 ARG cc_start: 0.8287 (mtm110) cc_final: 0.7962 (mtm110) REVERT: F 71 ASN cc_start: 0.8699 (t0) cc_final: 0.8458 (t0) REVERT: F 72 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8536 (tm) REVERT: F 87 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7188 (pp) REVERT: F 115 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7686 (mt-10) REVERT: F 144 PHE cc_start: 0.8672 (t80) cc_final: 0.8376 (t80) REVERT: F 158 VAL cc_start: 0.8521 (t) cc_final: 0.8126 (m) REVERT: F 214 PHE cc_start: 0.8651 (m-10) cc_final: 0.8392 (m-10) REVERT: F 240 LYS cc_start: 0.8631 (tppp) cc_final: 0.7934 (mtmp) REVERT: F 248 LYS cc_start: 0.8739 (mttt) cc_final: 0.7718 (mtpt) REVERT: G 61 ARG cc_start: 0.8258 (ptt180) cc_final: 0.7810 (ptt-90) REVERT: G 77 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8440 (ptpt) REVERT: G 80 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7465 (tptm) REVERT: G 116 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7923 (mmm) REVERT: G 132 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7210 (pp20) REVERT: G 147 ILE cc_start: 0.8855 (tt) cc_final: 0.8557 (mt) REVERT: G 199 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6823 (mpt) REVERT: G 222 SER cc_start: 0.8371 (m) cc_final: 0.7903 (t) REVERT: H 1 MET cc_start: 0.4462 (tpp) cc_final: 0.4209 (tpp) REVERT: H 162 CYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7402 (t) REVERT: H 196 THR cc_start: 0.8665 (p) cc_final: 0.8435 (t) REVERT: H 219 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7406 (t) REVERT: H 230 SER cc_start: 0.8975 (t) cc_final: 0.8755 (m) outliers start: 106 outliers final: 53 residues processed: 372 average time/residue: 0.4923 time to fit residues: 211.8599 Evaluate side-chains 358 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 286 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 233 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: 0.8980 chunk 12 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 170 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 37 HIS F 8 GLN F 213 ASN H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.159818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122311 restraints weight = 27127.093| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.00 r_work: 0.3319 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2847 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= 0.148 Angle : 0.577 9.775 30398 Z= 0.298 Chirality : 0.041 0.208 3528 Planarity : 0.004 0.072 3723 Dihedral : 15.993 172.681 3533 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.33 % Allowed : 21.82 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2623 helix: 1.21 (0.15), residues: 1268 sheet: -0.52 (0.22), residues: 509 loop : -0.31 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 264 TYR 0.016 0.002 TYR A 815 PHE 0.013 0.001 PHE A 692 TRP 0.012 0.001 TRP H 28 HIS 0.008 0.001 HIS H 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (22309) covalent geometry : angle 0.57676 / 0.30 (30398) hydrogen bonds : bond 0.03425 / 2.32 ( 1124) hydrogen bonds : angle 4.06004 / 2.92 ( 3210) *********************** 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 383 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 306 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 387 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 531 MET cc_start: 0.6498 (mmt) cc_final: 0.6021 (mmt) REVERT: A 541 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8039 (tt) REVERT: A 560 TYR cc_start: 0.8207 (m-80) cc_final: 0.7801 (m-80) REVERT: A 740 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.8018 (tp) REVERT: A 758 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8170 (tp) REVERT: A 822 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7561 (pp20) REVERT: A 852 LYS cc_start: 0.7941 (tppt) cc_final: 0.7561 (tttt) REVERT: A 853 MET cc_start: 0.7328 (ppp) cc_final: 0.6608 (mmm) REVERT: B 230 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.6879 (mtt90) REVERT: B 336 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: B 348 THR cc_start: 0.9049 (m) cc_final: 0.8579 (p) REVERT: C 50 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: C 130 MET cc_start: 0.9153 (mtm) cc_final: 0.8744 (mtp) REVERT: C 307 ASP cc_start: 0.8465 (m-30) cc_final: 0.8230 (m-30) REVERT: D 47 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8277 (mmtm) REVERT: D 209 GLN cc_start: 0.8460 (tt0) cc_final: 0.7940 (mt0) REVERT: D 288 LYS cc_start: 0.8601 (mptt) cc_final: 0.8386 (mtpt) REVERT: D 290 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: D 316 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.5280 (mp0) REVERT: E 11 CYS cc_start: 0.8191 (m) cc_final: 0.7874 (p) REVERT: E 83 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: E 139 LYS cc_start: 0.8926 (mtpp) cc_final: 0.8522 (mtpt) REVERT: F 1 MET cc_start: 0.7784 (tpp) cc_final: 0.7379 (tpt) REVERT: F 17 GLU cc_start: 0.7846 (tp30) cc_final: 0.7479 (tp30) REVERT: F 21 ASP cc_start: 0.7764 (t70) cc_final: 0.7343 (t0) REVERT: F 64 ARG cc_start: 0.8233 (mtm110) cc_final: 0.8027 (mtm110) REVERT: F 71 ASN cc_start: 0.8635 (t0) cc_final: 0.8397 (t0) REVERT: F 72 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8492 (tm) REVERT: F 87 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7191 (pp) REVERT: F 115 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7699 (mt-10) REVERT: F 144 PHE cc_start: 0.8662 (t80) cc_final: 0.8364 (t80) REVERT: F 214 PHE cc_start: 0.8635 (m-10) cc_final: 0.8403 (m-10) REVERT: F 240 LYS cc_start: 0.8581 (tppp) cc_final: 0.7851 (mtmp) REVERT: F 248 LYS cc_start: 0.8718 (mttt) cc_final: 0.7683 (mtpt) REVERT: G 61 ARG cc_start: 0.8247 (ptt180) cc_final: 0.7817 (ptt-90) REVERT: G 77 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8446 (ptpt) REVERT: G 80 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7507 (tptm) REVERT: G 116 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7956 (mmm) REVERT: G 132 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7141 (pp20) REVERT: G 147 ILE cc_start: 0.8816 (tt) cc_final: 0.8534 (mt) REVERT: G 222 SER cc_start: 0.8371 (m) cc_final: 0.7978 (t) REVERT: G 250 TYR cc_start: 0.8964 (m-80) cc_final: 0.7786 (m-80) REVERT: H 162 CYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7260 (t) REVERT: H 196 THR cc_start: 0.8718 (p) cc_final: 0.8476 (t) REVERT: H 230 SER cc_start: 0.8960 (t) cc_final: 0.8756 (m) outliers start: 77 outliers final: 39 residues processed: 355 average time/residue: 0.5417 time to fit residues: 220.7150 Evaluate side-chains 350 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 294 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 241 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 0.0020 chunk 140 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 788 GLN C 317 ASN F 8 GLN F 213 ASN F 246 HIS H 38 GLN H 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121001 restraints weight = 27241.542| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.92 r_work: 0.3293 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22309 Z= 0.147 Angle : 0.585 11.297 30398 Z= 0.300 Chirality : 0.041 0.196 3528 Planarity : 0.004 0.073 3723 Dihedral : 15.936 172.864 3531 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.60 % Allowed : 22.68 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.17), residues: 2623 helix: 1.28 (0.15), residues: 1269 sheet: -0.54 (0.22), residues: 517 loop : -0.24 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 264 TYR 0.020 0.002 TYR A 815 PHE 0.011 0.001 PHE A 692 TRP 0.011 0.001 TRP H 28 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (22309) covalent geometry : angle 0.58478 / 0.30 (30398) hydrogen bonds : bond 0.03332 / 2.25 ( 1124) hydrogen bonds : angle 4.01881 / 2.90 ( 3210) ********************** 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 363 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 303 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8074 (tm-30) REVERT: A 387 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8082 (mp) REVERT: A 531 MET cc_start: 0.6334 (mmt) cc_final: 0.5921 (mmt) REVERT: A 560 TYR cc_start: 0.8222 (m-80) cc_final: 0.7818 (m-80) REVERT: A 740 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7917 (tp) REVERT: A 758 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8162 (tp) REVERT: A 822 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7513 (pp20) REVERT: A 852 LYS cc_start: 0.7917 (tppt) cc_final: 0.7487 (tttt) REVERT: A 853 MET cc_start: 0.7272 (ppp) cc_final: 0.6555 (mmm) REVERT: B 230 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.6811 (mtt90) REVERT: C 50 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: C 130 MET cc_start: 0.9119 (mtm) cc_final: 0.8699 (mtp) REVERT: C 307 ASP cc_start: 0.8367 (m-30) cc_final: 0.8123 (m-30) REVERT: D 47 LYS cc_start: 0.8514 (mmtm) cc_final: 0.8257 (mmtm) REVERT: D 209 GLN cc_start: 0.8432 (tt0) cc_final: 0.7840 (mt0) REVERT: D 288 LYS cc_start: 0.8549 (mptt) cc_final: 0.8320 (mtpt) REVERT: D 290 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: D 316 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.5176 (mp0) REVERT: E 11 CYS cc_start: 0.8200 (m) cc_final: 0.7844 (p) REVERT: E 83 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6890 (tp30) REVERT: E 139 LYS cc_start: 0.8852 (mtpp) cc_final: 0.8436 (mtpt) REVERT: F 1 MET cc_start: 0.7736 (tpp) cc_final: 0.7293 (tpt) REVERT: F 17 GLU cc_start: 0.7773 (tp30) cc_final: 0.7272 (tp30) REVERT: F 21 ASP cc_start: 0.7674 (t70) cc_final: 0.7279 (t0) REVERT: F 53 ARG cc_start: 0.8361 (mpp80) cc_final: 0.7971 (mpp80) REVERT: F 64 ARG cc_start: 0.8258 (mtm110) cc_final: 0.8025 (mtm110) REVERT: F 71 ASN cc_start: 0.8637 (t0) cc_final: 0.8387 (t0) REVERT: F 72 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8465 (tm) REVERT: F 87 ILE cc_start: 0.7579 (mp) cc_final: 0.7184 (pp) REVERT: F 115 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7610 (mt-10) REVERT: F 144 PHE cc_start: 0.8681 (t80) cc_final: 0.8382 (t80) REVERT: F 158 VAL cc_start: 0.8582 (t) cc_final: 0.8252 (m) REVERT: F 240 LYS cc_start: 0.8559 (tppp) cc_final: 0.7819 (mtmp) REVERT: F 248 LYS cc_start: 0.8695 (mttt) cc_final: 0.7618 (mtpt) REVERT: G 61 ARG cc_start: 0.8145 (ptt180) cc_final: 0.7688 (ptt-90) REVERT: G 77 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8342 (ptpt) REVERT: G 80 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7501 (tptm) REVERT: G 116 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8055 (mmm) REVERT: G 132 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7203 (pp20) REVERT: G 147 ILE cc_start: 0.8804 (tt) cc_final: 0.8504 (mt) REVERT: G 222 SER cc_start: 0.8372 (m) cc_final: 0.7982 (t) REVERT: G 250 TYR cc_start: 0.8988 (m-80) cc_final: 0.7770 (m-80) REVERT: H 162 CYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7301 (t) REVERT: H 196 THR cc_start: 0.8671 (p) cc_final: 0.8437 (t) REVERT: H 224 THR cc_start: 0.8206 (t) cc_final: 0.7997 (m) REVERT: H 230 SER cc_start: 0.8942 (t) cc_final: 0.8720 (m) outliers start: 60 outliers final: 42 residues processed: 345 average time/residue: 0.5629 time to fit residues: 222.6213 Evaluate side-chains 348 residues out of total 2312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 116 MET Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 257 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 GLN B 118 ASN B 126 GLN E 213 HIS F 8 GLN F 213 ASN H 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.157412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118619 restraints weight = 27250.211| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.32 r_work: 0.3251 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 22309 Z= 0.273 Angle : 0.669 10.875 30398 Z= 0.340 Chirality : 0.045 0.205 3528 Planarity : 0.005 0.074 3723 Dihedral : 16.024 176.438 3531 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.07 % Allowed : 22.34 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2623 helix: 1.03 (0.14), residues: 1269 sheet: -0.57 (0.22), residues: 514 loop : -0.34 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 53 TYR 0.019 0.002 TYR A 815 PHE 0.019 0.002 PHE F 57 TRP 0.012 0.002 TRP H 28 HIS 0.006 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.27 (22309) covalent geometry : angle 0.66922 / 0.34 (30398) hydrogen bonds : bond 0.04009 / 2.71 ( 1124) hydrogen bonds : angle 4.18448 / 3.02 ( 3210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6756.95 seconds wall clock time: 115 minutes 48.86 seconds (6948.86 seconds total)