Starting phenix.real_space_refine on Sun Oct 12 02:57:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thd_41254/10_2025/8thd_41254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thd_41254/10_2025/8thd_41254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thd_41254/10_2025/8thd_41254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thd_41254/10_2025/8thd_41254.map" model { file = "/net/cci-nas-00/data/ceres_data/8thd_41254/10_2025/8thd_41254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thd_41254/10_2025/8thd_41254.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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 14 5.49 5 Mg 3 5.21 5 S 98 5.16 5 C 12905 2.51 5 N 3437 2.21 5 O 3939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20396 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3863 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain breaks: 4 Chain: "B" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2495 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2571 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2629 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 12, 'TRANS': 319} Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2675 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain breaks: 1 Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "G" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2011 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2003 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 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: 4.99, per 1000 atoms: 0.24 Number of scatterers: 20396 At special positions: 0 Unit cell: (115.92, 119.232, 150.696, 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 98 16.00 P 14 15.00 Mg 3 11.99 O 3939 8.00 N 3437 7.00 C 12905 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: 1.66 Conformation dependent library (CDL) restraints added in 834.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4898 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 16 sheets defined 50.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 256 through 276 removed outlier: 3.586A pdb=" N LYS A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 373 through 387 removed outlier: 6.616A pdb=" N ASP A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 429 Processing helix chain 'A' and resid 445 through 455 removed outlier: 3.514A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.521A pdb=" N VAL A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 Processing helix chain 'A' and resid 499 through 511 Processing helix chain 'A' and resid 535 through 557 removed outlier: 3.660A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 581 Processing helix chain 'A' and resid 585 through 592 removed outlier: 3.518A pdb=" N PHE A 592 " --> pdb=" O MET A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 629 removed outlier: 3.786A pdb=" N HIS A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 628 " --> pdb=" O GLN A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.996A pdb=" N ARG A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 661 Processing helix chain 'A' and resid 700 through 708 removed outlier: 4.138A pdb=" N LEU A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 716 Processing helix chain 'A' and resid 716 through 735 Processing helix chain 'A' and resid 773 through 781 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.052A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 4.027A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.742A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 150 " --> pdb=" O SER B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.786A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.671A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 88 through 102 removed outlier: 3.871A pdb=" N VAL C 92 " --> pdb=" O ARG C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.735A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 153' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.525A pdb=" N HIS C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.923A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.574A pdb=" N ILE C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.651A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 313 Processing helix chain 'C' and resid 315 through 334 removed outlier: 3.578A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 4.124A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 84 through 92 removed outlier: 4.344A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.519A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.844A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 removed outlier: 3.563A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.589A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.897A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 97 through 105 removed outlier: 7.971A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN E 104 " --> pdb=" O MET E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 119 removed outlier: 4.044A pdb=" N MET E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.517A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.720A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 245 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.092A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.257A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.624A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 166 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 221 removed outlier: 3.812A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.507A pdb=" N LYS G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) 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 80 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 221 Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.633A pdb=" N LYS H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 152 Processing helix 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 227 through 228 removed outlier: 3.749A pdb=" N VAL A 227 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.664A pdb=" N CYS A 438 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A 335 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR A 461 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N HIS A 337 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 600 through 601 removed outlier: 6.411A pdb=" N LEU A 600 " --> pdb=" O VAL E 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 77 removed outlier: 6.033A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.281A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 83 removed outlier: 6.116A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 Processing sheet with id=AA8, first strand: chain 'D' and resid 135 through 140 removed outlier: 5.544A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.498A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 57 through 60 removed outlier: 3.597A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 3.751A pdb=" N MET F 70 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL F 26 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 250 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR F 136 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS F 196 " --> pdb=" O SER F 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 204 through 208 removed outlier: 3.759A pdb=" N LEU F 205 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA F 171 " --> pdb=" O GLY F 178 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY F 178 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER F 177 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER F 179 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU G 113 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 100 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 2 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 3.792A pdb=" N MET G 70 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL G 26 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 206 through 208 removed outlier: 6.028A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE G 181 " --> pdb=" O ILE H 111 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE H 111 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU H 88 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU H 59 " --> pdb=" O LYS H 5 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 71 removed outlier: 5.936A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER H 230 " --> pdb=" O PRO H 234 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 139 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 177 through 182 removed outlier: 3.548A pdb=" N GLY H 178 " --> pdb=" O ALA H 171 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA H 171 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU H 205 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE H 162 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL H 203 " --> pdb=" O ILE H 162 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 3015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6749 1.36 - 1.51: 5016 1.51 - 1.65: 8806 1.65 - 1.80: 75 1.80 - 1.95: 77 Bond restraints: 20723 Sorted by residual: bond pdb=" C PRO D 132 " pdb=" O PRO D 132 " ideal model delta sigma weight residual 1.246 1.213 0.033 8.50e-03 1.38e+04 1.47e+01 bond pdb=" CA PRO D 132 " pdb=" C PRO D 132 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.23e+01 bond pdb=" N ARG D 101 " pdb=" CA ARG D 101 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.21e-02 6.83e+03 8.55e+00 bond pdb=" N GLY C 110 " pdb=" CA GLY C 110 " ideal model delta sigma weight residual 1.450 1.476 -0.026 9.10e-03 1.21e+04 8.11e+00 bond pdb=" N ILE E 96 " pdb=" CA ILE E 96 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.24e-02 6.50e+03 8.05e+00 ... (remaining 20718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 27441 1.96 - 3.92: 503 3.92 - 5.88: 76 5.88 - 7.83: 13 7.83 - 9.79: 5 Bond angle restraints: 28038 Sorted by residual: angle pdb=" CA ILE E 96 " pdb=" C ILE E 96 " pdb=" O ILE E 96 " ideal model delta sigma weight residual 121.64 117.90 3.74 9.80e-01 1.04e+00 1.46e+01 angle pdb=" N ILE F 128 " pdb=" CA ILE F 128 " pdb=" C ILE F 128 " ideal model delta sigma weight residual 111.91 108.62 3.29 8.90e-01 1.26e+00 1.37e+01 angle pdb=" N LYS G 20 " pdb=" CA LYS G 20 " pdb=" C LYS G 20 " ideal model delta sigma weight residual 111.02 115.53 -4.51 1.22e+00 6.72e-01 1.37e+01 angle pdb=" CA CYS H 81 " pdb=" C CYS H 81 " pdb=" O CYS H 81 " ideal model delta sigma weight residual 122.63 117.87 4.76 1.29e+00 6.01e-01 1.36e+01 angle pdb=" C GLN E 32 " pdb=" CA GLN E 32 " pdb=" CB GLN E 32 " ideal model delta sigma weight residual 110.33 113.95 -3.62 1.02e+00 9.61e-01 1.26e+01 ... (remaining 28033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 11840 25.07 - 50.14: 812 50.14 - 75.21: 133 75.21 - 100.28: 8 100.28 - 125.35: 1 Dihedral angle restraints: 12794 sinusoidal: 5292 harmonic: 7502 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 174.65 125.35 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" CA LEU D 58 " pdb=" C LEU D 58 " pdb=" N PRO D 59 " pdb=" CA PRO D 59 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE C 331 " pdb=" C PHE C 331 " pdb=" N GLU C 332 " pdb=" CA GLU C 332 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 12791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2729 0.054 - 0.107: 477 0.107 - 0.161: 77 0.161 - 0.215: 7 0.215 - 0.268: 1 Chirality restraints: 3291 Sorted by residual: chirality pdb=" CB ILE F 162 " pdb=" CA ILE F 162 " pdb=" CG1 ILE F 162 " pdb=" CG2 ILE F 162 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE E 96 " pdb=" N ILE E 96 " pdb=" C ILE E 96 " pdb=" CB ILE E 96 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ILE C 106 " pdb=" N ILE C 106 " pdb=" C ILE C 106 " pdb=" CB ILE C 106 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3288 not shown) Planarity restraints: 3551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 66 " 0.060 5.00e-02 4.00e+02 9.03e-02 1.31e+01 pdb=" N PRO D 67 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 196 " -0.044 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 197 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 144 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C CYS C 144 " -0.042 2.00e-02 2.50e+03 pdb=" O CYS C 144 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL C 145 " 0.014 2.00e-02 2.50e+03 ... (remaining 3548 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 301 2.67 - 3.22: 19112 3.22 - 3.78: 31860 3.78 - 4.34: 43124 4.34 - 4.90: 71679 Nonbonded interactions: 166076 Sorted by model distance: nonbonded pdb=" O GLY D 70 " pdb=" OG1 THR D 74 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.142 2.170 nonbonded pdb=" OD2 ASP D 140 " pdb="MG MG D 402 " model vdw 2.210 2.170 nonbonded pdb=" O LYS F 31 " pdb=" OH TYR F 60 " model vdw 2.252 3.040 nonbonded pdb=" O2B AGS D 401 " pdb="MG MG D 402 " model vdw 2.255 2.170 ... (remaining 166071 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 254) selection = (chain 'H' and resid 1 through 254) } 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: 6.980 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.880 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 20723 Z= 0.185 Angle : 0.652 9.794 28038 Z= 0.370 Chirality : 0.042 0.268 3291 Planarity : 0.005 0.090 3551 Dihedral : 16.149 125.349 7896 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.43 % Allowed : 18.06 % Favored : 81.50 % 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 aren not related in a simple way. whole: 0.17 (0.16), residues: 2527 helix: 1.22 (0.15), residues: 1144 sheet: 0.11 (0.25), residues: 471 loop : -1.28 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 149 TYR 0.016 0.001 TYR D 64 PHE 0.025 0.001 PHE A 509 TRP 0.009 0.001 TRP A 488 HIS 0.004 0.001 HIS D 124 Details of bonding type rmsd covalent geometry : bond 0.00312 (20723) covalent geometry : angle 0.65205 (28038) hydrogen bonds : bond 0.17325 ( 1047) hydrogen bonds : angle 6.77174 ( 3015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 653 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6582 (tp40) REVERT: A 359 ASN cc_start: 0.7637 (p0) cc_final: 0.7185 (t0) REVERT: A 361 TYR cc_start: 0.8663 (p90) cc_final: 0.8170 (p90) REVERT: A 505 MET cc_start: 0.8954 (tpp) cc_final: 0.8424 (mmt) REVERT: A 588 MET cc_start: 0.7567 (mmp) cc_final: 0.6882 (mtm) REVERT: C 15 TRP cc_start: 0.8650 (m-10) cc_final: 0.8228 (m-10) REVERT: C 30 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7671 (mm-40) REVERT: C 109 LYS cc_start: 0.6744 (OUTLIER) cc_final: 0.6031 (mptt) REVERT: D 49 LEU cc_start: 0.8525 (mt) cc_final: 0.8256 (mt) REVERT: D 83 TYR cc_start: 0.5684 (m-10) cc_final: 0.5181 (m-10) REVERT: D 132 PRO cc_start: 0.7948 (Cg_exo) cc_final: 0.7742 (Cg_endo) REVERT: D 134 TYR cc_start: 0.5532 (p90) cc_final: 0.5141 (p90) REVERT: D 343 LEU cc_start: 0.8749 (tp) cc_final: 0.8323 (tp) REVERT: F 70 MET cc_start: 0.1808 (mtp) cc_final: 0.1353 (mtp) REVERT: F 137 LEU cc_start: 0.1989 (pp) cc_final: 0.1704 (pp) REVERT: F 180 VAL cc_start: 0.2749 (t) cc_final: 0.2439 (m) REVERT: F 196 LYS cc_start: 0.3868 (mmtt) cc_final: 0.3565 (tptp) REVERT: G 8 GLU cc_start: 0.5159 (tp30) cc_final: 0.4905 (tm-30) REVERT: G 36 ILE cc_start: 0.6974 (pt) cc_final: 0.6738 (mt) REVERT: G 63 ASP cc_start: 0.4360 (p0) cc_final: 0.4106 (p0) REVERT: H 7 GLU cc_start: 0.6904 (mp0) cc_final: 0.6518 (tt0) REVERT: H 58 GLN cc_start: 0.7925 (tt0) cc_final: 0.7479 (mt0) REVERT: H 124 ASP cc_start: 0.6315 (t70) cc_final: 0.4742 (p0) REVERT: H 196 LYS cc_start: 0.6118 (mmtm) cc_final: 0.5737 (ttpp) outliers start: 10 outliers final: 2 residues processed: 660 average time/residue: 0.1682 time to fit residues: 164.6385 Evaluate side-chains 364 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 360 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN A 406 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN A 622 GLN B 108 HIS B 220 ASN D 42 GLN D 313 ASN E 18 HIS E 32 GLN G 94 ASN G 153 GLN H 29 GLN H 153 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.188099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125014 restraints weight = 28210.270| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.48 r_work: 0.3395 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20723 Z= 0.211 Angle : 0.680 11.415 28038 Z= 0.340 Chirality : 0.045 0.229 3291 Planarity : 0.005 0.056 3551 Dihedral : 7.602 115.351 2825 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.21 % Allowed : 17.85 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.16), residues: 2527 helix: 1.31 (0.15), residues: 1155 sheet: 0.03 (0.25), residues: 456 loop : -1.05 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 34 TYR 0.021 0.002 TYR D 160 PHE 0.029 0.002 PHE A 509 TRP 0.009 0.002 TRP A 420 HIS 0.005 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00505 (20723) covalent geometry : angle 0.68038 (28038) hydrogen bonds : bond 0.04475 ( 1047) hydrogen bonds : angle 5.07054 ( 3015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 387 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ASN cc_start: 0.7591 (p0) cc_final: 0.7209 (t0) REVERT: A 361 TYR cc_start: 0.8983 (p90) cc_final: 0.8538 (p90) REVERT: A 379 ASP cc_start: 0.7841 (m-30) cc_final: 0.7559 (m-30) REVERT: A 505 MET cc_start: 0.9031 (tpp) cc_final: 0.8460 (mmt) REVERT: A 588 MET cc_start: 0.7485 (mmp) cc_final: 0.6770 (mtm) REVERT: A 779 LYS cc_start: 0.7515 (mmmt) cc_final: 0.7275 (tppt) REVERT: B 115 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8140 (mt-10) REVERT: C 109 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.5868 (mptt) REVERT: C 139 LYS cc_start: 0.8882 (tppt) cc_final: 0.8563 (mptt) REVERT: C 140 ASN cc_start: 0.8001 (t0) cc_final: 0.7720 (t0) REVERT: C 316 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7757 (t0) REVERT: D 132 PRO cc_start: 0.8110 (Cg_exo) cc_final: 0.7532 (Cg_endo) REVERT: D 157 MET cc_start: 0.7136 (ptt) cc_final: 0.6633 (ptt) REVERT: D 249 LYS cc_start: 0.8537 (mttt) cc_final: 0.8044 (mtpt) REVERT: D 258 GLU cc_start: 0.7828 (tp30) cc_final: 0.7604 (pt0) REVERT: E 8 TYR cc_start: 0.8254 (m-80) cc_final: 0.7706 (m-10) REVERT: E 20 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7311 (tm-30) REVERT: E 71 ASP cc_start: 0.7496 (t0) cc_final: 0.7282 (t0) REVERT: E 174 MET cc_start: 0.8873 (tmm) cc_final: 0.8663 (ttp) REVERT: E 217 ASP cc_start: 0.8051 (t0) cc_final: 0.7767 (t0) REVERT: F 70 MET cc_start: 0.2013 (mtp) cc_final: 0.1488 (mtp) REVERT: F 174 ASP cc_start: 0.6625 (p0) cc_final: 0.6355 (m-30) REVERT: F 196 LYS cc_start: 0.4293 (mmtt) cc_final: 0.3850 (tptp) REVERT: F 249 PHE cc_start: 0.5545 (m-80) cc_final: 0.3948 (m-80) REVERT: G 1 MET cc_start: 0.3216 (mtt) cc_final: 0.2889 (mtt) REVERT: G 8 GLU cc_start: 0.5854 (tp30) cc_final: 0.5222 (tm-30) REVERT: G 63 ASP cc_start: 0.5339 (p0) cc_final: 0.5079 (p0) REVERT: G 149 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7439 (mtm-85) REVERT: G 190 HIS cc_start: 0.4815 (p90) cc_final: 0.4553 (p-80) REVERT: H 7 GLU cc_start: 0.7449 (mp0) cc_final: 0.6858 (tt0) REVERT: H 24 GLN cc_start: 0.8088 (tt0) cc_final: 0.7780 (mt0) REVERT: H 58 GLN cc_start: 0.8053 (tt0) cc_final: 0.7622 (mt0) REVERT: H 146 LYS cc_start: 0.8095 (tptm) cc_final: 0.7838 (tptm) REVERT: H 196 LYS cc_start: 0.5339 (mmtm) cc_final: 0.4985 (ttmm) REVERT: H 245 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6990 (p90) outliers start: 97 outliers final: 45 residues processed: 456 average time/residue: 0.1537 time to fit residues: 108.5734 Evaluate side-chains 363 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 315 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 73 LYS Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 146 optimal weight: 0.0770 chunk 174 optimal weight: 0.3980 chunk 222 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 41 ASN C 140 ASN D 313 ASN E 317 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.189280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127090 restraints weight = 28305.243| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.50 r_work: 0.3423 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20723 Z= 0.126 Angle : 0.566 10.376 28038 Z= 0.282 Chirality : 0.041 0.202 3291 Planarity : 0.004 0.042 3551 Dihedral : 7.290 115.473 2818 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.26 % Allowed : 19.50 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.17), residues: 2527 helix: 1.57 (0.15), residues: 1157 sheet: 0.10 (0.24), residues: 458 loop : -0.92 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 91 TYR 0.016 0.001 TYR D 134 PHE 0.022 0.001 PHE A 509 TRP 0.009 0.001 TRP B 11 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00288 (20723) covalent geometry : angle 0.56639 (28038) hydrogen bonds : bond 0.03816 ( 1047) hydrogen bonds : angle 4.73341 ( 3015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 348 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7181 (mp0) REVERT: A 361 TYR cc_start: 0.8912 (p90) cc_final: 0.8621 (p90) REVERT: A 379 ASP cc_start: 0.7751 (m-30) cc_final: 0.7495 (m-30) REVERT: A 383 ASP cc_start: 0.8024 (m-30) cc_final: 0.7820 (m-30) REVERT: A 505 MET cc_start: 0.8892 (tpp) cc_final: 0.8342 (mmt) REVERT: A 528 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6193 (tp) REVERT: A 588 MET cc_start: 0.7544 (mmp) cc_final: 0.6816 (mtm) REVERT: A 779 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7366 (tppt) REVERT: B 199 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7239 (mm-30) REVERT: C 71 TYR cc_start: 0.8234 (m-10) cc_final: 0.7917 (m-10) REVERT: C 99 ASP cc_start: 0.8568 (m-30) cc_final: 0.8323 (m-30) REVERT: C 109 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.5745 (mptt) REVERT: C 139 LYS cc_start: 0.8725 (tppt) cc_final: 0.8480 (mptt) REVERT: C 316 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7540 (t0) REVERT: D 188 ARG cc_start: 0.6799 (ttt-90) cc_final: 0.6470 (ttt-90) REVERT: E 100 ASP cc_start: 0.7661 (t0) cc_final: 0.7433 (t0) REVERT: F 126 LEU cc_start: 0.3041 (mt) cc_final: 0.2651 (tp) REVERT: F 174 ASP cc_start: 0.6589 (p0) cc_final: 0.6337 (m-30) REVERT: F 196 LYS cc_start: 0.4302 (mmtt) cc_final: 0.3830 (tptp) REVERT: F 249 PHE cc_start: 0.5445 (m-80) cc_final: 0.3881 (m-80) REVERT: G 1 MET cc_start: 0.3193 (mtt) cc_final: 0.2973 (mtt) REVERT: G 63 ASP cc_start: 0.5389 (p0) cc_final: 0.5179 (p0) REVERT: G 190 HIS cc_start: 0.4999 (p90) cc_final: 0.4682 (p-80) REVERT: H 7 GLU cc_start: 0.7371 (mp0) cc_final: 0.6859 (tt0) REVERT: H 24 GLN cc_start: 0.8111 (tt0) cc_final: 0.7843 (mt0) REVERT: H 44 ARG cc_start: 0.8294 (mtt90) cc_final: 0.8022 (mtt180) REVERT: H 58 GLN cc_start: 0.7942 (tt0) cc_final: 0.7706 (mt0) REVERT: H 80 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7443 (mtm110) REVERT: H 196 LYS cc_start: 0.5524 (mmtm) cc_final: 0.4984 (ttmm) REVERT: H 245 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.6942 (p90) outliers start: 75 outliers final: 44 residues processed: 404 average time/residue: 0.1501 time to fit residues: 94.0848 Evaluate side-chains 356 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 308 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 94 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 711 GLN B 250 GLN C 210 ASN D 25 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.131149 restraints weight = 28118.003| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.80 r_work: 0.3234 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20723 Z= 0.229 Angle : 0.653 12.109 28038 Z= 0.327 Chirality : 0.045 0.248 3291 Planarity : 0.004 0.075 3551 Dihedral : 7.474 117.580 2818 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.73 % Allowed : 19.54 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.16), residues: 2527 helix: 1.32 (0.15), residues: 1158 sheet: -0.12 (0.24), residues: 473 loop : -0.90 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 157 TYR 0.022 0.002 TYR B 15 PHE 0.022 0.002 PHE A 509 TRP 0.011 0.002 TRP A 510 HIS 0.005 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00552 (20723) covalent geometry : angle 0.65343 (28038) hydrogen bonds : bond 0.04471 ( 1047) hydrogen bonds : angle 4.72853 ( 3015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 337 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8766 (tp) REVERT: A 462 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6935 (mttt) REVERT: A 505 MET cc_start: 0.8842 (tpp) cc_final: 0.8314 (mmt) REVERT: A 528 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6161 (tp) REVERT: A 588 MET cc_start: 0.7740 (mmp) cc_final: 0.7092 (mtm) REVERT: A 779 LYS cc_start: 0.7814 (mmmt) cc_final: 0.7398 (tppt) REVERT: B 94 LYS cc_start: 0.9164 (ttpp) cc_final: 0.8959 (tttp) REVERT: B 204 GLN cc_start: 0.8831 (tp40) cc_final: 0.8545 (tp-100) REVERT: C 99 ASP cc_start: 0.8433 (m-30) cc_final: 0.8233 (m-30) REVERT: C 109 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.5887 (mptt) REVERT: C 139 LYS cc_start: 0.8761 (tppt) cc_final: 0.8529 (mptt) REVERT: C 230 ASP cc_start: 0.7895 (t0) cc_final: 0.7650 (m-30) REVERT: C 316 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7718 (t0) REVERT: D 61 MET cc_start: 0.7456 (pmm) cc_final: 0.6828 (ptt) REVERT: D 81 GLU cc_start: 0.7363 (mp0) cc_final: 0.7161 (mt-10) REVERT: D 134 TYR cc_start: 0.5346 (p90) cc_final: 0.4942 (p90) REVERT: D 188 ARG cc_start: 0.7033 (ttt-90) cc_final: 0.6803 (ttt-90) REVERT: E 249 LYS cc_start: 0.7739 (mtpp) cc_final: 0.7188 (mmmt) REVERT: F 126 LEU cc_start: 0.3118 (mt) cc_final: 0.2727 (tp) REVERT: F 174 ASP cc_start: 0.6635 (p0) cc_final: 0.6363 (m-30) REVERT: F 196 LYS cc_start: 0.4282 (mmtt) cc_final: 0.3838 (tptp) REVERT: F 246 LEU cc_start: 0.7560 (tt) cc_final: 0.7245 (tt) REVERT: F 249 PHE cc_start: 0.5402 (m-80) cc_final: 0.3772 (m-80) REVERT: G 1 MET cc_start: 0.3573 (mtt) cc_final: 0.3140 (mtt) REVERT: G 190 HIS cc_start: 0.5034 (p90) cc_final: 0.4829 (p90) REVERT: H 7 GLU cc_start: 0.7646 (mp0) cc_final: 0.6799 (pm20) REVERT: H 24 GLN cc_start: 0.8242 (tt0) cc_final: 0.7957 (mt0) REVERT: H 44 ARG cc_start: 0.8498 (mtt90) cc_final: 0.8222 (mtt180) REVERT: H 58 GLN cc_start: 0.8187 (tt0) cc_final: 0.7638 (mt0) REVERT: H 161 MET cc_start: 0.6099 (ttt) cc_final: 0.5764 (ttt) REVERT: H 196 LYS cc_start: 0.5638 (mmtm) cc_final: 0.5053 (ttmm) REVERT: H 245 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7368 (p90) outliers start: 109 outliers final: 68 residues processed: 422 average time/residue: 0.1514 time to fit residues: 98.4616 Evaluate side-chains 367 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 293 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 249 LYS Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 333 SER Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 241 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN B 250 GLN D 25 GLN D 321 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.185668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128413 restraints weight = 28139.109| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.82 r_work: 0.3355 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20723 Z= 0.134 Angle : 0.559 8.482 28038 Z= 0.277 Chirality : 0.041 0.201 3291 Planarity : 0.004 0.033 3551 Dihedral : 7.325 116.246 2818 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.56 % Allowed : 21.15 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.17), residues: 2527 helix: 1.60 (0.15), residues: 1159 sheet: -0.03 (0.24), residues: 467 loop : -0.78 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 80 TYR 0.023 0.002 TYR H 211 PHE 0.024 0.002 PHE A 509 TRP 0.009 0.001 TRP A 266 HIS 0.004 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00313 (20723) covalent geometry : angle 0.55875 (28038) hydrogen bonds : bond 0.03655 ( 1047) hydrogen bonds : angle 4.51370 ( 3015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 315 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8026 (mmt-90) cc_final: 0.7807 (mmt-90) REVERT: A 505 MET cc_start: 0.8747 (tpp) cc_final: 0.8311 (mmt) REVERT: A 528 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6097 (tp) REVERT: A 588 MET cc_start: 0.7579 (mmp) cc_final: 0.6944 (mtm) REVERT: A 779 LYS cc_start: 0.7748 (mmmt) cc_final: 0.7403 (tppt) REVERT: B 94 LYS cc_start: 0.9061 (ttpp) cc_final: 0.8846 (tttp) REVERT: C 99 ASP cc_start: 0.8600 (m-30) cc_final: 0.8362 (m-30) REVERT: C 109 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.5913 (mptt) REVERT: C 139 LYS cc_start: 0.8791 (tppt) cc_final: 0.8561 (mptt) REVERT: C 205 MET cc_start: 0.8572 (mmm) cc_final: 0.8331 (mmt) REVERT: C 316 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7515 (t0) REVERT: D 36 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8108 (tp) REVERT: D 131 CYS cc_start: 0.8285 (p) cc_final: 0.7276 (t) REVERT: D 134 TYR cc_start: 0.5348 (p90) cc_final: 0.5076 (p90) REVERT: D 188 ARG cc_start: 0.7031 (ttt-90) cc_final: 0.6813 (ttt-90) REVERT: E 8 TYR cc_start: 0.8173 (m-80) cc_final: 0.7621 (m-10) REVERT: E 67 ARG cc_start: 0.8296 (mtp-110) cc_final: 0.8071 (mtt90) REVERT: E 224 GLN cc_start: 0.8755 (tt0) cc_final: 0.8375 (mt0) REVERT: F 126 LEU cc_start: 0.3108 (mt) cc_final: 0.2742 (tp) REVERT: F 174 ASP cc_start: 0.6748 (p0) cc_final: 0.6493 (m-30) REVERT: F 196 LYS cc_start: 0.4308 (mmtt) cc_final: 0.3877 (tptp) REVERT: F 246 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7293 (tt) REVERT: F 249 PHE cc_start: 0.5339 (m-80) cc_final: 0.3786 (m-80) REVERT: G 190 HIS cc_start: 0.5083 (p90) cc_final: 0.4657 (p-80) REVERT: H 7 GLU cc_start: 0.7652 (mp0) cc_final: 0.6767 (pm20) REVERT: H 24 GLN cc_start: 0.8281 (tt0) cc_final: 0.7979 (mt0) REVERT: H 58 GLN cc_start: 0.8069 (tt0) cc_final: 0.7626 (mt0) REVERT: H 80 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7540 (mtm110) REVERT: H 122 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.7038 (p0) REVERT: H 124 ASP cc_start: 0.6888 (t70) cc_final: 0.5491 (p0) REVERT: H 144 PHE cc_start: 0.5554 (t80) cc_final: 0.4950 (t80) REVERT: H 196 LYS cc_start: 0.5502 (mmtm) cc_final: 0.4983 (ttmm) REVERT: H 245 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.7211 (p90) outliers start: 82 outliers final: 54 residues processed: 378 average time/residue: 0.1497 time to fit residues: 87.9590 Evaluate side-chains 345 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 284 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 213 optimal weight: 0.1980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 ASN B 220 ASN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.183255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132887 restraints weight = 28083.025| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.80 r_work: 0.3286 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20723 Z= 0.189 Angle : 0.594 10.825 28038 Z= 0.294 Chirality : 0.042 0.235 3291 Planarity : 0.004 0.044 3551 Dihedral : 7.376 115.817 2818 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.26 % Allowed : 21.28 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.17), residues: 2527 helix: 1.60 (0.15), residues: 1159 sheet: -0.10 (0.24), residues: 470 loop : -0.76 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 157 TYR 0.021 0.002 TYR H 211 PHE 0.033 0.002 PHE G 19 TRP 0.009 0.001 TRP B 11 HIS 0.003 0.001 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00455 (20723) covalent geometry : angle 0.59378 (28038) hydrogen bonds : bond 0.03880 ( 1047) hydrogen bonds : angle 4.49761 ( 3015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 285 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8085 (mmt-90) cc_final: 0.7830 (mmt-90) REVERT: A 505 MET cc_start: 0.8765 (tpp) cc_final: 0.8262 (mmt) REVERT: A 528 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6194 (tp) REVERT: A 575 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8758 (tppt) REVERT: A 588 MET cc_start: 0.7680 (mmp) cc_final: 0.7050 (mtm) REVERT: A 779 LYS cc_start: 0.7810 (mmmt) cc_final: 0.7374 (tppt) REVERT: C 99 ASP cc_start: 0.8589 (m-30) cc_final: 0.8357 (m-30) REVERT: C 109 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.5926 (mptt) REVERT: C 139 LYS cc_start: 0.8762 (tppt) cc_final: 0.8530 (mptt) REVERT: C 316 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7595 (t0) REVERT: D 131 CYS cc_start: 0.8445 (p) cc_final: 0.7418 (t) REVERT: D 134 TYR cc_start: 0.5340 (p90) cc_final: 0.5132 (p90) REVERT: D 145 MET cc_start: 0.1614 (mmm) cc_final: 0.1397 (mmt) REVERT: D 188 ARG cc_start: 0.7106 (ttt-90) cc_final: 0.6876 (ttt-90) REVERT: E 67 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.8204 (mtt90) REVERT: E 224 GLN cc_start: 0.8724 (tt0) cc_final: 0.8397 (mt0) REVERT: F 50 LEU cc_start: 0.8029 (pp) cc_final: 0.7553 (mt) REVERT: F 126 LEU cc_start: 0.3138 (mt) cc_final: 0.2740 (tp) REVERT: F 174 ASP cc_start: 0.6748 (p0) cc_final: 0.6469 (m-30) REVERT: F 196 LYS cc_start: 0.4304 (mmtt) cc_final: 0.3826 (tptp) REVERT: F 246 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.6876 (tt) REVERT: F 249 PHE cc_start: 0.5332 (m-80) cc_final: 0.3689 (m-80) REVERT: G 8 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6921 (mp0) REVERT: H 7 GLU cc_start: 0.7720 (mp0) cc_final: 0.6860 (pm20) REVERT: H 24 GLN cc_start: 0.8274 (tt0) cc_final: 0.8000 (mt0) REVERT: H 55 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: H 58 GLN cc_start: 0.8176 (tt0) cc_final: 0.7608 (mt0) REVERT: H 80 ARG cc_start: 0.7971 (ttp-110) cc_final: 0.7641 (mtm110) REVERT: H 122 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.7001 (p0) REVERT: H 124 ASP cc_start: 0.7014 (t70) cc_final: 0.5657 (p0) REVERT: H 196 LYS cc_start: 0.5536 (mmtm) cc_final: 0.4916 (ttmm) REVERT: H 245 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7409 (p90) outliers start: 98 outliers final: 70 residues processed: 360 average time/residue: 0.1529 time to fit residues: 85.2454 Evaluate side-chains 351 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 273 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 7 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 36 optimal weight: 0.0470 chunk 185 optimal weight: 9.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.183534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130248 restraints weight = 28174.354| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.75 r_work: 0.3356 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20723 Z= 0.113 Angle : 0.542 10.634 28038 Z= 0.269 Chirality : 0.041 0.266 3291 Planarity : 0.004 0.048 3551 Dihedral : 7.245 114.027 2818 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.30 % Allowed : 22.41 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.17), residues: 2527 helix: 1.79 (0.15), residues: 1157 sheet: -0.05 (0.24), residues: 470 loop : -0.73 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 154 TYR 0.017 0.001 TYR H 211 PHE 0.046 0.001 PHE G 19 TRP 0.008 0.001 TRP A 266 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00259 (20723) covalent geometry : angle 0.54211 (28038) hydrogen bonds : bond 0.03368 ( 1047) hydrogen bonds : angle 4.36933 ( 3015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 310 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6840 (mttt) REVERT: A 505 MET cc_start: 0.8714 (tpp) cc_final: 0.8259 (mmt) REVERT: A 575 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8665 (tppt) REVERT: A 588 MET cc_start: 0.7616 (mmp) cc_final: 0.6947 (mtm) REVERT: A 779 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7362 (tppt) REVERT: B 204 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8437 (tp-100) REVERT: C 109 LYS cc_start: 0.6747 (OUTLIER) cc_final: 0.5999 (mptt) REVERT: C 139 LYS cc_start: 0.8848 (tppt) cc_final: 0.8606 (mptt) REVERT: C 316 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7488 (t0) REVERT: D 131 CYS cc_start: 0.8413 (p) cc_final: 0.7150 (t) REVERT: D 132 PRO cc_start: 0.7930 (Cg_exo) cc_final: 0.7619 (Cg_endo) REVERT: D 134 TYR cc_start: 0.5333 (p90) cc_final: 0.5117 (p90) REVERT: D 145 MET cc_start: 0.1557 (mmm) cc_final: 0.1330 (mmt) REVERT: D 188 ARG cc_start: 0.7053 (ttt-90) cc_final: 0.6844 (ttt-90) REVERT: E 8 TYR cc_start: 0.8212 (m-80) cc_final: 0.7657 (m-10) REVERT: E 224 GLN cc_start: 0.8702 (tt0) cc_final: 0.8368 (mt0) REVERT: F 126 LEU cc_start: 0.3138 (mt) cc_final: 0.2761 (tp) REVERT: F 196 LYS cc_start: 0.4266 (mmtt) cc_final: 0.3825 (tptp) REVERT: F 246 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7230 (tt) REVERT: F 249 PHE cc_start: 0.5277 (m-80) cc_final: 0.3712 (m-80) REVERT: G 8 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7037 (mp0) REVERT: G 25 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.6819 (mt) REVERT: H 7 GLU cc_start: 0.7718 (mp0) cc_final: 0.6903 (pm20) REVERT: H 24 GLN cc_start: 0.8243 (tt0) cc_final: 0.7934 (mt0) REVERT: H 55 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: H 58 GLN cc_start: 0.8092 (tt0) cc_final: 0.7609 (mt0) REVERT: H 80 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7615 (mtm110) REVERT: H 122 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6955 (p0) REVERT: H 124 ASP cc_start: 0.6936 (t70) cc_final: 0.5568 (p0) REVERT: H 196 LYS cc_start: 0.5491 (mmtm) cc_final: 0.4882 (ttmm) outliers start: 76 outliers final: 55 residues processed: 368 average time/residue: 0.1465 time to fit residues: 83.8214 Evaluate side-chains 354 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 291 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 243 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.185727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.136338 restraints weight = 28313.227| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.02 r_work: 0.3334 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20723 Z= 0.130 Angle : 0.562 10.032 28038 Z= 0.276 Chirality : 0.041 0.256 3291 Planarity : 0.004 0.047 3551 Dihedral : 7.213 113.514 2818 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.56 % Allowed : 22.32 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.17), residues: 2527 helix: 1.84 (0.15), residues: 1156 sheet: 0.01 (0.24), residues: 470 loop : -0.70 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.016 0.001 TYR D 83 PHE 0.039 0.001 PHE G 19 TRP 0.009 0.001 TRP A 266 HIS 0.004 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00307 (20723) covalent geometry : angle 0.56154 (28038) hydrogen bonds : bond 0.03418 ( 1047) hydrogen bonds : angle 4.32715 ( 3015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 306 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.8209 (mmt-90) cc_final: 0.7864 (mmp80) REVERT: A 462 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6975 (mttt) REVERT: A 486 ASP cc_start: 0.7530 (m-30) cc_final: 0.7252 (t0) REVERT: A 505 MET cc_start: 0.8686 (tpp) cc_final: 0.8194 (mmt) REVERT: A 528 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6069 (tp) REVERT: A 575 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8743 (tppt) REVERT: A 588 MET cc_start: 0.7653 (mmp) cc_final: 0.7052 (mtm) REVERT: B 204 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8448 (tp-100) REVERT: B 321 ASN cc_start: 0.7505 (m-40) cc_final: 0.7278 (m110) REVERT: C 109 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.5990 (mptt) REVERT: C 139 LYS cc_start: 0.8791 (tppt) cc_final: 0.8547 (mptt) REVERT: C 316 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7531 (t0) REVERT: D 61 MET cc_start: 0.7590 (pmm) cc_final: 0.6923 (ptp) REVERT: D 83 TYR cc_start: 0.7371 (m-10) cc_final: 0.7154 (m-10) REVERT: D 131 CYS cc_start: 0.8453 (p) cc_final: 0.7245 (t) REVERT: D 157 MET cc_start: 0.7034 (ptt) cc_final: 0.6808 (ptt) REVERT: D 188 ARG cc_start: 0.7100 (ttt-90) cc_final: 0.6883 (ttt-90) REVERT: E 8 TYR cc_start: 0.8210 (m-80) cc_final: 0.7647 (m-10) REVERT: E 224 GLN cc_start: 0.8738 (tt0) cc_final: 0.8405 (mt0) REVERT: F 126 LEU cc_start: 0.3138 (mt) cc_final: 0.2759 (tp) REVERT: F 196 LYS cc_start: 0.4273 (mmtt) cc_final: 0.3833 (tptp) REVERT: F 249 PHE cc_start: 0.5244 (m-80) cc_final: 0.3643 (m-80) REVERT: H 7 GLU cc_start: 0.7624 (mp0) cc_final: 0.6799 (pm20) REVERT: H 24 GLN cc_start: 0.8255 (tt0) cc_final: 0.7975 (mt0) REVERT: H 55 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: H 58 GLN cc_start: 0.8080 (tt0) cc_final: 0.7627 (mt0) REVERT: H 80 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7544 (mtm110) REVERT: H 122 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.7023 (p0) REVERT: H 124 ASP cc_start: 0.7030 (t70) cc_final: 0.5599 (p0) REVERT: H 196 LYS cc_start: 0.5707 (mmtm) cc_final: 0.5058 (ttmm) REVERT: H 245 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7397 (p90) outliers start: 82 outliers final: 63 residues processed: 368 average time/residue: 0.1523 time to fit residues: 87.0990 Evaluate side-chains 362 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 291 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 125 optimal weight: 6.9990 chunk 40 optimal weight: 0.0770 chunk 175 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN D 25 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.185741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135784 restraints weight = 28203.531| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.91 r_work: 0.3344 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20723 Z= 0.136 Angle : 0.564 9.432 28038 Z= 0.278 Chirality : 0.041 0.187 3291 Planarity : 0.004 0.047 3551 Dihedral : 7.188 113.357 2818 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.34 % Allowed : 22.75 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.17), residues: 2527 helix: 1.84 (0.15), residues: 1156 sheet: 0.07 (0.24), residues: 471 loop : -0.69 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 165 TYR 0.019 0.001 TYR D 134 PHE 0.023 0.001 PHE A 722 TRP 0.008 0.001 TRP A 266 HIS 0.003 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00320 (20723) covalent geometry : angle 0.56416 (28038) hydrogen bonds : bond 0.03427 ( 1047) hydrogen bonds : angle 4.31636 ( 3015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 292 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 ASP cc_start: 0.7502 (m-30) cc_final: 0.7223 (t0) REVERT: A 505 MET cc_start: 0.8661 (tpp) cc_final: 0.8159 (mmt) REVERT: A 528 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6105 (tp) REVERT: A 575 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8757 (tppt) REVERT: A 588 MET cc_start: 0.7671 (mmp) cc_final: 0.7073 (mtm) REVERT: C 109 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.5982 (mptt) REVERT: C 139 LYS cc_start: 0.8811 (tppt) cc_final: 0.8570 (mptt) REVERT: C 316 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7539 (t0) REVERT: D 131 CYS cc_start: 0.8427 (p) cc_final: 0.7396 (t) REVERT: D 188 ARG cc_start: 0.7125 (ttt-90) cc_final: 0.6910 (ttt-90) REVERT: E 8 TYR cc_start: 0.8186 (m-80) cc_final: 0.7620 (m-10) REVERT: E 224 GLN cc_start: 0.8726 (tt0) cc_final: 0.8403 (mt0) REVERT: F 126 LEU cc_start: 0.3218 (mt) cc_final: 0.2815 (tp) REVERT: F 196 LYS cc_start: 0.4221 (mmtt) cc_final: 0.3780 (tptp) REVERT: F 239 PHE cc_start: 0.4051 (m-80) cc_final: 0.3734 (t80) REVERT: F 249 PHE cc_start: 0.5283 (m-80) cc_final: 0.3684 (m-80) REVERT: H 7 GLU cc_start: 0.7675 (mp0) cc_final: 0.6825 (pm20) REVERT: H 24 GLN cc_start: 0.8224 (tt0) cc_final: 0.7956 (mt0) REVERT: H 55 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: H 58 GLN cc_start: 0.8088 (tt0) cc_final: 0.7633 (mt0) REVERT: H 80 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7512 (mtm110) REVERT: H 122 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.7030 (p0) REVERT: H 124 ASP cc_start: 0.7092 (t70) cc_final: 0.5576 (p0) REVERT: H 196 LYS cc_start: 0.5631 (mmtm) cc_final: 0.5001 (ttmm) REVERT: H 245 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7419 (p90) outliers start: 77 outliers final: 64 residues processed: 351 average time/residue: 0.1513 time to fit residues: 81.6493 Evaluate side-chains 351 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 280 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 29 optimal weight: 0.9990 chunk 215 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS H 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.185912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128708 restraints weight = 28231.747| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.69 r_work: 0.3357 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20723 Z= 0.124 Angle : 0.568 9.273 28038 Z= 0.279 Chirality : 0.041 0.274 3291 Planarity : 0.004 0.047 3551 Dihedral : 7.157 113.287 2818 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.30 % Allowed : 23.06 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.17), residues: 2527 helix: 1.86 (0.15), residues: 1156 sheet: 0.08 (0.24), residues: 471 loop : -0.65 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.036 0.001 TYR D 83 PHE 0.041 0.001 PHE G 19 TRP 0.010 0.001 TRP A 266 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00289 (20723) covalent geometry : angle 0.56772 (28038) hydrogen bonds : bond 0.03348 ( 1047) hydrogen bonds : angle 4.30792 ( 3015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5054 Ramachandran restraints generated. 2527 Oldfield, 0 Emsley, 2527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 292 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 ASP cc_start: 0.7469 (m-30) cc_final: 0.7192 (t0) REVERT: A 505 MET cc_start: 0.8728 (tpp) cc_final: 0.8213 (mmt) REVERT: A 528 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5958 (tp) REVERT: A 575 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8631 (tppt) REVERT: A 588 MET cc_start: 0.7652 (mmp) cc_final: 0.7031 (mtm) REVERT: C 109 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6068 (mptt) REVERT: C 316 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7427 (t0) REVERT: D 131 CYS cc_start: 0.8492 (p) cc_final: 0.7593 (t) REVERT: D 157 MET cc_start: 0.6868 (ptt) cc_final: 0.5972 (tpp) REVERT: D 188 ARG cc_start: 0.7180 (ttt-90) cc_final: 0.6964 (ttt-90) REVERT: E 8 TYR cc_start: 0.8216 (m-80) cc_final: 0.7651 (m-10) REVERT: E 224 GLN cc_start: 0.8708 (tt0) cc_final: 0.8335 (mt0) REVERT: F 126 LEU cc_start: 0.3214 (mt) cc_final: 0.2829 (tp) REVERT: F 196 LYS cc_start: 0.4262 (mmtt) cc_final: 0.3821 (tptp) REVERT: F 239 PHE cc_start: 0.3886 (m-80) cc_final: 0.3581 (t80) REVERT: F 249 PHE cc_start: 0.5318 (m-80) cc_final: 0.3773 (m-80) REVERT: G 165 GLU cc_start: 0.5679 (tp30) cc_final: 0.5129 (tm-30) REVERT: H 7 GLU cc_start: 0.7719 (mp0) cc_final: 0.6820 (pm20) REVERT: H 24 GLN cc_start: 0.8215 (tt0) cc_final: 0.7867 (mt0) REVERT: H 55 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: H 58 GLN cc_start: 0.8089 (tt0) cc_final: 0.7591 (mt0) REVERT: H 80 ARG cc_start: 0.7948 (ttp-110) cc_final: 0.7554 (mtm110) REVERT: H 122 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6961 (p0) REVERT: H 124 ASP cc_start: 0.7061 (t70) cc_final: 0.5517 (p0) REVERT: H 196 LYS cc_start: 0.5524 (mmtm) cc_final: 0.4908 (ttmm) REVERT: H 245 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.7206 (p90) outliers start: 76 outliers final: 60 residues processed: 351 average time/residue: 0.1467 time to fit residues: 80.4912 Evaluate side-chains 349 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 282 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 243 SER Chi-restraints excluded: chain H residue 245 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 180 optimal weight: 30.0000 chunk 96 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.183058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132863 restraints weight = 28267.766| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.91 r_work: 0.3304 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20723 Z= 0.195 Angle : 0.609 9.095 28038 Z= 0.302 Chirality : 0.043 0.230 3291 Planarity : 0.004 0.050 3551 Dihedral : 7.337 115.077 2818 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.47 % Allowed : 23.10 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.17), residues: 2527 helix: 1.70 (0.15), residues: 1158 sheet: 0.01 (0.24), residues: 471 loop : -0.67 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 154 TYR 0.016 0.002 TYR H 211 PHE 0.019 0.002 PHE A 722 TRP 0.009 0.002 TRP A 510 HIS 0.007 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00469 (20723) covalent geometry : angle 0.60894 (28038) hydrogen bonds : bond 0.03861 ( 1047) hydrogen bonds : angle 4.42897 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5598.77 seconds wall clock time: 96 minutes 42.76 seconds (5802.76 seconds total)