Starting phenix.real_space_refine on Sun Aug 24 11:48:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iin_60598/08_2025/9iin_60598.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iin_60598/08_2025/9iin_60598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iin_60598/08_2025/9iin_60598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iin_60598/08_2025/9iin_60598.map" model { file = "/net/cci-nas-00/data/ceres_data/9iin_60598/08_2025/9iin_60598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iin_60598/08_2025/9iin_60598.cif" } resolution = 3.2 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 2 5.21 5 S 130 5.16 5 C 12466 2.51 5 N 3409 2.21 5 O 3755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19773 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3660 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 29, 'TRANS': 431} Chain breaks: 5 Chain: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2492 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "C" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2533 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 2310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2310 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 4 Chain: "E" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2750 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "F" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1954 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain breaks: 1 Chain: "G" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1980 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "H" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 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, 'ATP': 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, 'ATP': 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: 3.49, per 1000 atoms: 0.18 Number of scatterers: 19773 At special positions: 0 Unit cell: (119.97, 118.11, 132.99, 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 130 16.00 P 11 15.00 Mg 2 11.99 O 3755 8.00 N 3409 7.00 C 12466 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: 1.50 Conformation dependent library (CDL) restraints added in 599.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 14 sheets defined 53.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.516A pdb=" N LEU A 294 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 removed outlier: 4.202A pdb=" N LEU A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LYS A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP A 307 " --> pdb=" O CYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 removed outlier: 4.161A pdb=" N ALA A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.994A pdb=" N ALA A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.565A pdb=" N GLU A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 503 removed outlier: 3.964A pdb=" N GLN A 500 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 530 removed outlier: 3.651A pdb=" N LEU A 527 " --> pdb=" O GLN A 523 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 548 through 556 removed outlier: 3.907A pdb=" N ASN A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 556 " --> pdb=" O CYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 removed outlier: 4.290A pdb=" N VAL A 589 " --> pdb=" O GLY A 585 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.701A pdb=" N HIS A 637 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 656 Processing helix chain 'A' and resid 665 through 689 removed outlier: 3.562A pdb=" N HIS A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 698 removed outlier: 3.775A pdb=" N ARG A 696 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 697 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Proline residue: A 698 - end of helix Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.227A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 743 removed outlier: 4.083A pdb=" N GLY A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 Processing helix chain 'A' and resid 761 through 767 removed outlier: 3.741A pdb=" N LEU A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 787 Processing helix chain 'A' and resid 788 through 799 Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 837 through 855 removed outlier: 3.512A pdb=" N MET A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.660A pdb=" N ILE B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.825A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.693A pdb=" N MET B 146 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.191A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 194 through 210 Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 228 through 244 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 306 removed outlier: 4.066A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 329 Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.687A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 79 through 86 removed outlier: 4.156A pdb=" N GLY C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 178 through 193 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 291 Processing helix chain 'C' and resid 294 through 314 removed outlier: 3.658A pdb=" N SER C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 338 removed outlier: 4.181A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG C 333 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 45 Processing helix chain 'D' and resid 56 through 65 removed outlier: 3.979A pdb=" N ALA D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 82 Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.778A pdb=" N LEU D 129 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 181 through 185 removed outlier: 3.667A pdb=" N SER D 184 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 3.642A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 234 Processing helix chain 'D' and resid 239 through 253 removed outlier: 3.651A pdb=" N THR D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.581A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 removed outlier: 3.535A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 316 removed outlier: 3.909A pdb=" N GLU D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 96 through 102 removed outlier: 6.725A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 120 removed outlier: 3.852A pdb=" N GLN E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 220 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.645A pdb=" N HIS E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 301 removed outlier: 3.729A pdb=" N HIS E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 327 through 348 removed outlier: 4.025A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 21 removed outlier: 4.358A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 81 removed outlier: 3.965A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.654A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.847A pdb=" N LYS G 13 " --> pdb=" O GLY G 9 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP G 21 " --> pdb=" O GLU 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 155 removed outlier: 3.865A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing helix chain 'H' and resid 8 through 20 removed outlier: 4.453A pdb=" N LEU H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU H 17 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 80 removed outlier: 3.599A pdb=" N LYS H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.819A pdb=" N HIS H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 219 No H-bonds generated for 'chain 'H' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 397 Processing sheet with id=AA3, first strand: chain 'A' and resid 803 through 807 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.381A pdb=" N LEU B 103 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 91 removed outlier: 6.494A pdb=" N LEU C 88 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP C 125 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU C 90 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.637A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 145 through 147 removed outlier: 6.297A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 68 through 74 removed outlier: 6.604A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.592A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL G 203 " --> pdb=" O CYS G 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 8.211A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY F 245 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 204 through 208 removed outlier: 5.275A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN F 177 " --> pdb=" O GLU H 115 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU H 115 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS F 181 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL H 111 " --> pdb=" O LYS F 181 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL H 102 " --> pdb=" O THR H 89 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR H 59 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 59 through 60 removed outlier: 3.730A pdb=" N ASN H 177 " --> pdb=" O GLU G 115 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER H 172 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA H 157 " --> pdb=" O SER H 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 7.494A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SER G 230 " --> pdb=" O PRO G 234 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 69 through 71 removed outlier: 6.657A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER H 39 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 48 " --> pdb=" O SER H 39 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N SER H 230 " --> pdb=" O PRO H 234 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) 1076 hydrogen bonds defined for protein. 3063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6538 1.34 - 1.46: 3008 1.46 - 1.58: 10320 1.58 - 1.69: 19 1.69 - 1.81: 200 Bond restraints: 20085 Sorted by residual: bond pdb=" CB PRO A 771 " pdb=" CG PRO A 771 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.85e+00 bond pdb=" CG1 ILE C 284 " pdb=" CD1 ILE C 284 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.18e+00 bond pdb=" CB GLU A 847 " pdb=" CG GLU A 847 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CG GLU A 847 " pdb=" CD GLU A 847 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.65e+00 bond pdb=" CB ARG D 105 " pdb=" CG ARG D 105 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.53e+00 ... (remaining 20080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 26522 1.70 - 3.39: 503 3.39 - 5.09: 106 5.09 - 6.78: 26 6.78 - 8.48: 7 Bond angle restraints: 27164 Sorted by residual: angle pdb=" N GLU A 847 " pdb=" CA GLU A 847 " pdb=" CB GLU A 847 " ideal model delta sigma weight residual 110.22 116.77 -6.55 1.54e+00 4.22e-01 1.81e+01 angle pdb=" CA GLU A 847 " pdb=" CB GLU A 847 " pdb=" CG GLU A 847 " ideal model delta sigma weight residual 114.10 122.16 -8.06 2.00e+00 2.50e-01 1.62e+01 angle pdb=" CA PRO A 771 " pdb=" N PRO A 771 " pdb=" CD PRO A 771 " ideal model delta sigma weight residual 112.00 106.58 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" CB GLU A 847 " pdb=" CG GLU A 847 " pdb=" CD GLU A 847 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.70e+00 3.46e-01 1.49e+01 angle pdb=" C GLU D 168 " pdb=" N LYS D 169 " pdb=" CA LYS D 169 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 ... (remaining 27159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.30: 12028 27.30 - 54.60: 375 54.60 - 81.90: 26 81.90 - 109.19: 7 109.19 - 136.49: 1 Dihedral angle restraints: 12437 sinusoidal: 5123 harmonic: 7314 Sorted by residual: dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 76.49 -136.49 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" CA ILE D 186 " pdb=" C ILE D 186 " pdb=" N ILE D 187 " pdb=" CA ILE D 187 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA MET F 119 " pdb=" C MET F 119 " pdb=" N ASP F 120 " pdb=" CA ASP F 120 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 12434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2449 0.045 - 0.089: 544 0.089 - 0.134: 166 0.134 - 0.178: 9 0.178 - 0.223: 2 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CB ILE G 128 " pdb=" CA ILE G 128 " pdb=" CG1 ILE G 128 " pdb=" CG2 ILE G 128 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA GLU A 847 " pdb=" N GLU A 847 " pdb=" C GLU A 847 " pdb=" CB GLU A 847 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA GLU D 188 " pdb=" N GLU D 188 " pdb=" C GLU D 188 " pdb=" CB GLU D 188 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 3167 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 279 " 0.017 2.00e-02 2.50e+03 1.82e-02 6.64e+00 pdb=" CG TYR B 279 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 279 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 279 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 279 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 279 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 279 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 279 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 188 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO D 189 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 189 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 189 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 126 " -0.019 2.00e-02 2.50e+03 1.65e-02 4.78e+00 pdb=" CG PHE D 126 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE D 126 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE D 126 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 126 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 126 " -0.000 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 272 2.58 - 3.16: 17351 3.16 - 3.74: 32259 3.74 - 4.32: 42883 4.32 - 4.90: 70714 Nonbonded interactions: 163479 Sorted by model distance: nonbonded pdb="MG MG C 401 " pdb=" O3G ATP C 402 " model vdw 2.005 2.170 nonbonded pdb="MG MG B 401 " pdb=" O1B ATP B 402 " model vdw 2.046 2.170 nonbonded pdb="MG MG C 401 " pdb=" O1B ATP C 402 " model vdw 2.089 2.170 nonbonded pdb="MG MG C 401 " pdb=" O1A ATP C 402 " model vdw 2.093 2.170 nonbonded pdb=" OG1 THR C 67 " pdb="MG MG C 401 " model vdw 2.137 2.170 ... (remaining 163474 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 189 or resid 191 through 255)) selection = (chain 'H' and (resid 1 through 189 or resid 191 through 255)) } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 14.100 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 0.110 20085 Z= 0.140 Angle : 0.612 8.475 27164 Z= 0.321 Chirality : 0.041 0.223 3170 Planarity : 0.004 0.057 3456 Dihedral : 12.590 136.494 7673 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 1.22 (0.18), residues: 2464 helix: 1.62 (0.16), residues: 1139 sheet: 0.59 (0.24), residues: 478 loop : -0.07 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 146 TYR 0.045 0.002 TYR B 279 PHE 0.037 0.001 PHE D 126 TRP 0.025 0.001 TRP H 28 HIS 0.012 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00314 (20085) covalent geometry : angle 0.61189 (27164) hydrogen bonds : bond 0.19739 ( 1076) hydrogen bonds : angle 7.02996 ( 3063) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7791 (t70) cc_final: 0.7568 (t70) REVERT: A 473 ARG cc_start: 0.9081 (ptt90) cc_final: 0.8846 (ppt90) REVERT: A 730 MET cc_start: 0.9233 (tpp) cc_final: 0.8889 (tpp) REVERT: A 847 GLU cc_start: 0.8885 (mp0) cc_final: 0.8653 (mp0) REVERT: B 175 ASP cc_start: 0.8689 (p0) cc_final: 0.8347 (p0) REVERT: B 176 LYS cc_start: 0.9297 (mmtp) cc_final: 0.9016 (mmmm) REVERT: C 90 LEU cc_start: 0.9131 (mt) cc_final: 0.8762 (mp) REVERT: D 229 TYR cc_start: 0.8907 (t80) cc_final: 0.8531 (t80) REVERT: E 110 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9104 (mm-30) REVERT: E 111 MET cc_start: 0.9485 (mmp) cc_final: 0.9175 (mmm) REVERT: F 17 GLU cc_start: 0.8820 (tp30) cc_final: 0.8560 (tp30) REVERT: F 38 GLN cc_start: 0.7980 (tt0) cc_final: 0.7728 (tt0) REVERT: G 1 MET cc_start: 0.8355 (tpp) cc_final: 0.7255 (tpp) REVERT: G 38 GLN cc_start: 0.9016 (tt0) cc_final: 0.8700 (tt0) REVERT: G 119 MET cc_start: 0.8231 (mmm) cc_final: 0.8012 (mmm) REVERT: H 2 PHE cc_start: 0.8773 (t80) cc_final: 0.8559 (t80) REVERT: H 90 LEU cc_start: 0.9028 (tp) cc_final: 0.8691 (tp) REVERT: H 204 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8699 (mp-120) REVERT: H 214 PHE cc_start: 0.9313 (m-10) cc_final: 0.8844 (m-80) REVERT: H 244 MET cc_start: 0.8857 (ppp) cc_final: 0.8087 (tmm) REVERT: H 250 TYR cc_start: 0.8967 (m-80) cc_final: 0.8606 (m-80) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1440 time to fit residues: 54.6429 Evaluate side-chains 196 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 50.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 GLN A 713 HIS A 738 GLN B 182 GLN B 298 ASN ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 361 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.081679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055446 restraints weight = 76046.942| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.92 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20085 Z= 0.281 Angle : 0.689 10.306 27164 Z= 0.356 Chirality : 0.045 0.185 3170 Planarity : 0.005 0.052 3456 Dihedral : 7.679 141.726 2803 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.02 % Favored : 95.94 % Rotamer: Outliers : 0.78 % Allowed : 7.81 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.18), residues: 2464 helix: 1.44 (0.15), residues: 1155 sheet: 0.21 (0.23), residues: 511 loop : -0.17 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 634 TYR 0.033 0.002 TYR B 279 PHE 0.020 0.002 PHE G 169 TRP 0.014 0.002 TRP H 28 HIS 0.010 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00606 (20085) covalent geometry : angle 0.68851 (27164) hydrogen bonds : bond 0.04651 ( 1076) hydrogen bonds : angle 5.55970 ( 3063) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7801 (t70) cc_final: 0.7588 (t70) REVERT: A 473 ARG cc_start: 0.9133 (ptt90) cc_final: 0.8914 (ppt90) REVERT: A 524 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: B 175 ASP cc_start: 0.9006 (p0) cc_final: 0.8657 (p0) REVERT: B 176 LYS cc_start: 0.9538 (mmtp) cc_final: 0.9171 (mmmm) REVERT: B 308 MET cc_start: 0.8557 (ppp) cc_final: 0.8199 (ppp) REVERT: C 90 LEU cc_start: 0.9156 (mt) cc_final: 0.8868 (mp) REVERT: D 172 LYS cc_start: 0.9254 (ptmm) cc_final: 0.8861 (tmtt) REVERT: E 106 VAL cc_start: 0.9649 (m) cc_final: 0.9031 (p) REVERT: E 110 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9110 (mm-30) REVERT: F 17 GLU cc_start: 0.9249 (tp30) cc_final: 0.8998 (tp30) REVERT: F 68 MET cc_start: 0.8931 (ppp) cc_final: 0.8518 (ppp) REVERT: G 1 MET cc_start: 0.8399 (tpp) cc_final: 0.7494 (tpp) REVERT: G 38 GLN cc_start: 0.9092 (tt0) cc_final: 0.8667 (tt0) REVERT: G 117 LYS cc_start: 0.8212 (mttt) cc_final: 0.7974 (mttt) REVERT: G 146 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8530 (mmm-85) REVERT: H 1 MET cc_start: 0.8998 (tpt) cc_final: 0.8709 (tpp) REVERT: H 90 LEU cc_start: 0.9033 (tp) cc_final: 0.8788 (tp) REVERT: H 204 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8576 (tm-30) REVERT: H 214 PHE cc_start: 0.9317 (m-10) cc_final: 0.8848 (m-80) REVERT: H 244 MET cc_start: 0.9117 (ppp) cc_final: 0.8513 (tmm) outliers start: 17 outliers final: 8 residues processed: 218 average time/residue: 0.1543 time to fit residues: 49.7180 Evaluate side-chains 191 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 162 optimal weight: 0.9990 chunk 89 optimal weight: 0.0170 chunk 16 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 336 GLN C 132 GLN D 125 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS E 265 GLN F 49 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.083835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.057456 restraints weight = 75538.688| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 5.03 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20085 Z= 0.124 Angle : 0.594 9.198 27164 Z= 0.303 Chirality : 0.042 0.161 3170 Planarity : 0.004 0.052 3456 Dihedral : 7.388 142.261 2803 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 1.01 % Allowed : 9.18 % Favored : 89.81 % 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: 0.96 (0.17), residues: 2464 helix: 1.53 (0.15), residues: 1155 sheet: 0.15 (0.22), residues: 509 loop : -0.21 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 751 TYR 0.033 0.001 TYR B 279 PHE 0.017 0.001 PHE G 215 TRP 0.020 0.001 TRP H 28 HIS 0.010 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00267 (20085) covalent geometry : angle 0.59377 (27164) hydrogen bonds : bond 0.03814 ( 1076) hydrogen bonds : angle 5.09450 ( 3063) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7801 (t70) cc_final: 0.7569 (t70) REVERT: A 473 ARG cc_start: 0.9154 (ptt90) cc_final: 0.8892 (ppt90) REVERT: A 509 HIS cc_start: 0.8312 (t70) cc_final: 0.7355 (m-70) REVERT: A 730 MET cc_start: 0.9441 (tpp) cc_final: 0.8984 (tpp) REVERT: B 175 ASP cc_start: 0.8973 (p0) cc_final: 0.8628 (p0) REVERT: B 176 LYS cc_start: 0.9551 (mmtp) cc_final: 0.9145 (mmmm) REVERT: B 308 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8210 (ppp) REVERT: C 90 LEU cc_start: 0.9208 (mt) cc_final: 0.8903 (mp) REVERT: C 213 MET cc_start: 0.8409 (tpt) cc_final: 0.8017 (tpp) REVERT: D 172 LYS cc_start: 0.9231 (ptmm) cc_final: 0.8877 (tmtt) REVERT: E 110 GLU cc_start: 0.9505 (mm-30) cc_final: 0.9043 (pt0) REVERT: E 111 MET cc_start: 0.9431 (mmm) cc_final: 0.8792 (mmm) REVERT: E 201 LYS cc_start: 0.9634 (tppt) cc_final: 0.9352 (mmtm) REVERT: F 17 GLU cc_start: 0.9205 (tp30) cc_final: 0.8922 (tp30) REVERT: F 40 MET cc_start: 0.8468 (tpp) cc_final: 0.8141 (tpt) REVERT: F 68 MET cc_start: 0.8743 (ppp) cc_final: 0.8333 (ppp) REVERT: F 244 MET cc_start: 0.8810 (mmm) cc_final: 0.8330 (mmm) REVERT: G 38 GLN cc_start: 0.9043 (tt0) cc_final: 0.8598 (tt0) REVERT: G 49 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7796 (tm-30) REVERT: G 117 LYS cc_start: 0.8314 (mttt) cc_final: 0.8057 (mttt) REVERT: G 211 TYR cc_start: 0.9244 (m-80) cc_final: 0.8886 (m-80) REVERT: H 1 MET cc_start: 0.9014 (tpt) cc_final: 0.8687 (tpp) REVERT: H 16 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9112 (mm) REVERT: H 91 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8377 (mmm-85) REVERT: H 153 HIS cc_start: 0.9386 (m170) cc_final: 0.8992 (m-70) REVERT: H 211 TYR cc_start: 0.8832 (m-80) cc_final: 0.8621 (m-80) REVERT: H 214 PHE cc_start: 0.9311 (m-10) cc_final: 0.8781 (m-80) REVERT: H 244 MET cc_start: 0.9128 (ppp) cc_final: 0.8732 (tmm) outliers start: 22 outliers final: 10 residues processed: 235 average time/residue: 0.1346 time to fit residues: 47.2757 Evaluate side-chains 204 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 29 optimal weight: 10.0000 chunk 214 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 118 ASN B 298 ASN ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.082829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.056353 restraints weight = 76045.564| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 5.04 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20085 Z= 0.189 Angle : 0.608 9.408 27164 Z= 0.309 Chirality : 0.042 0.157 3170 Planarity : 0.004 0.051 3456 Dihedral : 7.222 140.061 2803 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 1.28 % Allowed : 10.69 % Favored : 88.03 % 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: 0.98 (0.17), residues: 2464 helix: 1.59 (0.15), residues: 1163 sheet: 0.07 (0.22), residues: 510 loop : -0.23 (0.24), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 210 TYR 0.033 0.002 TYR B 279 PHE 0.028 0.001 PHE F 215 TRP 0.008 0.001 TRP F 28 HIS 0.005 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00404 (20085) covalent geometry : angle 0.60759 (27164) hydrogen bonds : bond 0.03668 ( 1076) hydrogen bonds : angle 4.96020 ( 3063) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7839 (t70) cc_final: 0.7603 (t70) REVERT: A 473 ARG cc_start: 0.9171 (ptt90) cc_final: 0.8863 (ppt90) REVERT: A 509 HIS cc_start: 0.8248 (t70) cc_final: 0.7318 (m-70) REVERT: B 175 ASP cc_start: 0.9027 (p0) cc_final: 0.8719 (p0) REVERT: B 176 LYS cc_start: 0.9562 (mmtp) cc_final: 0.9152 (mmmm) REVERT: B 308 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8150 (ppp) REVERT: C 90 LEU cc_start: 0.9203 (mt) cc_final: 0.8894 (mp) REVERT: C 213 MET cc_start: 0.8446 (tpt) cc_final: 0.8057 (tpp) REVERT: D 172 LYS cc_start: 0.9253 (ptmm) cc_final: 0.8900 (tmtt) REVERT: E 110 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9106 (mm-30) REVERT: E 111 MET cc_start: 0.9468 (mmm) cc_final: 0.9223 (mmm) REVERT: E 194 HIS cc_start: 0.8898 (t70) cc_final: 0.8624 (t70) REVERT: E 201 LYS cc_start: 0.9629 (tppt) cc_final: 0.9346 (mmtm) REVERT: F 17 GLU cc_start: 0.9191 (tp30) cc_final: 0.8894 (tp30) REVERT: F 68 MET cc_start: 0.8760 (ppp) cc_final: 0.8437 (ppp) REVERT: F 75 MET cc_start: 0.9670 (mmm) cc_final: 0.9118 (tpp) REVERT: F 116 MET cc_start: 0.8691 (ttm) cc_final: 0.7951 (ttm) REVERT: F 244 MET cc_start: 0.8717 (mmm) cc_final: 0.8331 (mmm) REVERT: G 1 MET cc_start: 0.8517 (tpp) cc_final: 0.8135 (tpp) REVERT: G 38 GLN cc_start: 0.9022 (tt0) cc_final: 0.8516 (tt0) REVERT: G 45 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8760 (m) REVERT: G 49 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7822 (tm-30) REVERT: G 211 TYR cc_start: 0.9268 (m-80) cc_final: 0.8693 (m-80) REVERT: H 1 MET cc_start: 0.9048 (tpt) cc_final: 0.8597 (tpp) REVERT: H 61 ARG cc_start: 0.9014 (ppt170) cc_final: 0.8592 (ptm-80) REVERT: H 91 ARG cc_start: 0.8556 (mmm-85) cc_final: 0.8300 (mmm-85) REVERT: H 153 HIS cc_start: 0.9371 (m170) cc_final: 0.8972 (m-70) REVERT: H 211 TYR cc_start: 0.8856 (m-80) cc_final: 0.8639 (m-80) REVERT: H 214 PHE cc_start: 0.9301 (m-10) cc_final: 0.8778 (m-80) REVERT: H 244 MET cc_start: 0.9139 (ppp) cc_final: 0.8769 (tmm) outliers start: 28 outliers final: 13 residues processed: 220 average time/residue: 0.1431 time to fit residues: 47.4941 Evaluate side-chains 205 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 101 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 225 optimal weight: 5.9990 chunk 221 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 108 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 298 ASN C 76 GLN ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.081380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.054780 restraints weight = 76740.841| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.98 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 20085 Z= 0.282 Angle : 0.669 9.229 27164 Z= 0.339 Chirality : 0.043 0.155 3170 Planarity : 0.004 0.059 3456 Dihedral : 7.305 142.864 2803 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 1.51 % Allowed : 12.01 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.17), residues: 2464 helix: 1.45 (0.15), residues: 1159 sheet: -0.12 (0.23), residues: 490 loop : -0.28 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 64 TYR 0.032 0.002 TYR B 279 PHE 0.032 0.002 PHE G 215 TRP 0.015 0.001 TRP H 28 HIS 0.009 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00599 (20085) covalent geometry : angle 0.66864 (27164) hydrogen bonds : bond 0.03877 ( 1076) hydrogen bonds : angle 5.03441 ( 3063) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7832 (t70) cc_final: 0.7574 (t70) REVERT: A 473 ARG cc_start: 0.9164 (ptt90) cc_final: 0.8872 (ppt90) REVERT: B 175 ASP cc_start: 0.9105 (p0) cc_final: 0.8788 (p0) REVERT: B 176 LYS cc_start: 0.9577 (mmtp) cc_final: 0.9175 (mmmm) REVERT: B 229 MET cc_start: 0.9007 (tpp) cc_final: 0.8684 (tpp) REVERT: C 90 LEU cc_start: 0.9171 (mt) cc_final: 0.8848 (mp) REVERT: C 213 MET cc_start: 0.8489 (tpt) cc_final: 0.8108 (tpp) REVERT: D 172 LYS cc_start: 0.9254 (ptmm) cc_final: 0.8906 (tmtt) REVERT: E 110 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9104 (mm-30) REVERT: E 111 MET cc_start: 0.9472 (mmm) cc_final: 0.9220 (mmm) REVERT: E 194 HIS cc_start: 0.8951 (t70) cc_final: 0.8679 (t70) REVERT: F 17 GLU cc_start: 0.9243 (tp30) cc_final: 0.8951 (tp30) REVERT: F 75 MET cc_start: 0.9664 (mmm) cc_final: 0.9080 (tpp) REVERT: F 116 MET cc_start: 0.8731 (ttm) cc_final: 0.7816 (ttm) REVERT: G 1 MET cc_start: 0.8660 (tpp) cc_final: 0.8418 (tpp) REVERT: G 38 GLN cc_start: 0.8976 (tt0) cc_final: 0.8461 (tt0) REVERT: H 1 MET cc_start: 0.9103 (tpt) cc_final: 0.8574 (tpp) REVERT: H 40 MET cc_start: 0.7808 (tpp) cc_final: 0.7559 (tpp) REVERT: H 61 ARG cc_start: 0.9120 (ppt170) cc_final: 0.8778 (ptm-80) REVERT: H 79 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9278 (mm) REVERT: H 91 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8303 (mmm-85) REVERT: H 131 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8068 (pp30) REVERT: H 153 HIS cc_start: 0.9337 (m170) cc_final: 0.8955 (m-70) REVERT: H 211 TYR cc_start: 0.8891 (m-80) cc_final: 0.8657 (m-80) REVERT: H 214 PHE cc_start: 0.9322 (m-10) cc_final: 0.8751 (m-80) REVERT: H 232 ASP cc_start: 0.8722 (m-30) cc_final: 0.8214 (t0) REVERT: H 244 MET cc_start: 0.9129 (ppp) cc_final: 0.8787 (tmm) outliers start: 33 outliers final: 22 residues processed: 218 average time/residue: 0.1418 time to fit residues: 47.0080 Evaluate side-chains 210 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 143 optimal weight: 0.1980 chunk 132 optimal weight: 2.9990 chunk 204 optimal weight: 20.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 ASN A 713 HIS B 298 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.082663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.056477 restraints weight = 75531.936| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 4.96 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20085 Z= 0.149 Angle : 0.597 9.814 27164 Z= 0.301 Chirality : 0.041 0.149 3170 Planarity : 0.004 0.055 3456 Dihedral : 7.194 143.309 2803 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.65 % Favored : 96.31 % Rotamer: Outliers : 1.51 % Allowed : 12.61 % Favored : 85.88 % 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: 0.92 (0.17), residues: 2464 helix: 1.62 (0.15), residues: 1156 sheet: -0.13 (0.22), residues: 498 loop : -0.27 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 149 TYR 0.034 0.001 TYR B 279 PHE 0.034 0.001 PHE G 215 TRP 0.018 0.001 TRP H 28 HIS 0.003 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00321 (20085) covalent geometry : angle 0.59698 (27164) hydrogen bonds : bond 0.03401 ( 1076) hydrogen bonds : angle 4.76414 ( 3063) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7817 (t70) cc_final: 0.7557 (t-170) REVERT: A 473 ARG cc_start: 0.9162 (ptt90) cc_final: 0.8855 (ppt90) REVERT: A 524 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: B 175 ASP cc_start: 0.9071 (p0) cc_final: 0.8771 (p0) REVERT: B 176 LYS cc_start: 0.9578 (mmtp) cc_final: 0.9174 (mmmm) REVERT: B 229 MET cc_start: 0.9049 (tpp) cc_final: 0.8779 (tpp) REVERT: B 308 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8240 (ppp) REVERT: C 90 LEU cc_start: 0.9203 (mt) cc_final: 0.8963 (mp) REVERT: C 213 MET cc_start: 0.8411 (tpt) cc_final: 0.8039 (tpp) REVERT: C 225 MET cc_start: 0.8695 (tmm) cc_final: 0.8441 (tmm) REVERT: D 172 LYS cc_start: 0.9256 (ptmm) cc_final: 0.8889 (tmtt) REVERT: D 356 MET cc_start: 0.8910 (ttt) cc_final: 0.8613 (ttt) REVERT: E 110 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9106 (mm-30) REVERT: E 111 MET cc_start: 0.9517 (mmm) cc_final: 0.9250 (mmm) REVERT: E 194 HIS cc_start: 0.8951 (t70) cc_final: 0.8681 (t70) REVERT: E 201 LYS cc_start: 0.9638 (tppt) cc_final: 0.9352 (mmtm) REVERT: E 213 HIS cc_start: 0.9051 (m90) cc_final: 0.8699 (m90) REVERT: E 292 MET cc_start: 0.9238 (mmm) cc_final: 0.8994 (mmm) REVERT: F 17 GLU cc_start: 0.9192 (tp30) cc_final: 0.8901 (tp30) REVERT: F 68 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8312 (ppp) REVERT: F 75 MET cc_start: 0.9703 (mmm) cc_final: 0.9016 (tpp) REVERT: F 116 MET cc_start: 0.8567 (ttm) cc_final: 0.6777 (ttm) REVERT: F 125 GLN cc_start: 0.9179 (tt0) cc_final: 0.8776 (tm-30) REVERT: F 199 MET cc_start: 0.9144 (tmm) cc_final: 0.8921 (tpp) REVERT: G 1 MET cc_start: 0.8925 (tpp) cc_final: 0.8431 (tpp) REVERT: G 38 GLN cc_start: 0.8975 (tt0) cc_final: 0.8403 (tt0) REVERT: G 49 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7839 (tm-30) REVERT: G 211 TYR cc_start: 0.9134 (m-80) cc_final: 0.8829 (m-80) REVERT: H 1 MET cc_start: 0.9110 (tpt) cc_final: 0.8661 (tpp) REVERT: H 40 MET cc_start: 0.7928 (tpp) cc_final: 0.7615 (tpp) REVERT: H 61 ARG cc_start: 0.9128 (ppt170) cc_final: 0.8660 (ptm-80) REVERT: H 79 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9375 (mm) REVERT: H 91 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8320 (mmm-85) REVERT: H 153 HIS cc_start: 0.9333 (m170) cc_final: 0.8965 (m-70) REVERT: H 210 ARG cc_start: 0.8990 (mmp80) cc_final: 0.8781 (mmp80) REVERT: H 214 PHE cc_start: 0.9295 (m-10) cc_final: 0.8821 (m-80) REVERT: H 232 ASP cc_start: 0.8719 (m-30) cc_final: 0.8256 (t0) outliers start: 33 outliers final: 21 residues processed: 225 average time/residue: 0.1465 time to fit residues: 49.8118 Evaluate side-chains 215 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 177 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 4 optimal weight: 50.0000 chunk 182 optimal weight: 8.9990 chunk 236 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.080640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.053721 restraints weight = 77574.600| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 5.02 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 20085 Z= 0.342 Angle : 0.715 9.466 27164 Z= 0.361 Chirality : 0.044 0.198 3170 Planarity : 0.004 0.053 3456 Dihedral : 7.300 142.352 2803 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.71 % Favored : 95.25 % Rotamer: Outliers : 1.92 % Allowed : 13.34 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.17), residues: 2464 helix: 1.38 (0.15), residues: 1160 sheet: -0.25 (0.23), residues: 491 loop : -0.33 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 149 TYR 0.036 0.002 TYR G 249 PHE 0.040 0.002 PHE F 215 TRP 0.019 0.002 TRP H 28 HIS 0.009 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00725 (20085) covalent geometry : angle 0.71475 (27164) hydrogen bonds : bond 0.03949 ( 1076) hydrogen bonds : angle 5.01284 ( 3063) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7890 (t70) cc_final: 0.7660 (t-170) REVERT: A 473 ARG cc_start: 0.9154 (ptt90) cc_final: 0.8872 (ppt90) REVERT: A 524 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: B 176 LYS cc_start: 0.9592 (mmtp) cc_final: 0.9267 (mmmm) REVERT: B 308 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8178 (ppp) REVERT: C 90 LEU cc_start: 0.9174 (mt) cc_final: 0.8928 (mp) REVERT: C 213 MET cc_start: 0.8535 (tpt) cc_final: 0.8163 (tpp) REVERT: D 172 LYS cc_start: 0.9270 (ptmm) cc_final: 0.8929 (tmtt) REVERT: D 356 MET cc_start: 0.8976 (ttt) cc_final: 0.8443 (ttt) REVERT: E 110 GLU cc_start: 0.9526 (mm-30) cc_final: 0.9155 (mm-30) REVERT: E 194 HIS cc_start: 0.9018 (t70) cc_final: 0.8783 (t-90) REVERT: E 201 LYS cc_start: 0.9621 (tppt) cc_final: 0.9327 (mmtm) REVERT: E 292 MET cc_start: 0.9300 (mmm) cc_final: 0.9043 (mmm) REVERT: F 17 GLU cc_start: 0.9241 (tp30) cc_final: 0.8918 (tp30) REVERT: F 68 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8258 (ppp) REVERT: F 75 MET cc_start: 0.9664 (mmm) cc_final: 0.9074 (tpp) REVERT: F 116 MET cc_start: 0.8739 (ttm) cc_final: 0.7747 (ttm) REVERT: F 125 GLN cc_start: 0.9144 (tt0) cc_final: 0.8706 (tm-30) REVERT: F 215 PHE cc_start: 0.8999 (m-80) cc_final: 0.8752 (m-80) REVERT: F 249 TYR cc_start: 0.9257 (m-80) cc_final: 0.8462 (m-80) REVERT: G 38 GLN cc_start: 0.8953 (tt0) cc_final: 0.8457 (tt0) REVERT: G 57 PHE cc_start: 0.8615 (m-80) cc_final: 0.8038 (t80) REVERT: H 1 MET cc_start: 0.9139 (tpt) cc_final: 0.8782 (tpp) REVERT: H 40 MET cc_start: 0.8028 (tpp) cc_final: 0.7700 (tpp) REVERT: H 61 ARG cc_start: 0.9193 (ppt170) cc_final: 0.8895 (ptm160) REVERT: H 79 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9332 (mm) REVERT: H 91 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.8280 (mmm-85) REVERT: H 153 HIS cc_start: 0.9328 (m170) cc_final: 0.8975 (m-70) REVERT: H 214 PHE cc_start: 0.9309 (m-10) cc_final: 0.8877 (m-80) REVERT: H 244 MET cc_start: 0.8765 (tmm) cc_final: 0.8530 (tmm) outliers start: 42 outliers final: 27 residues processed: 223 average time/residue: 0.1354 time to fit residues: 46.1707 Evaluate side-chains 219 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 298 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.082344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.055755 restraints weight = 75578.730| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 5.02 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20085 Z= 0.159 Angle : 0.628 10.153 27164 Z= 0.312 Chirality : 0.042 0.157 3170 Planarity : 0.004 0.056 3456 Dihedral : 7.207 143.807 2803 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 1.83 % Allowed : 13.39 % Favored : 84.79 % 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: 0.86 (0.17), residues: 2464 helix: 1.59 (0.15), residues: 1162 sheet: -0.21 (0.22), residues: 495 loop : -0.31 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 210 TYR 0.037 0.002 TYR B 279 PHE 0.044 0.001 PHE G 215 TRP 0.010 0.001 TRP H 28 HIS 0.004 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00348 (20085) covalent geometry : angle 0.62794 (27164) hydrogen bonds : bond 0.03456 ( 1076) hydrogen bonds : angle 4.73270 ( 3063) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7924 (t70) cc_final: 0.7663 (t-170) REVERT: A 473 ARG cc_start: 0.9153 (ptt90) cc_final: 0.8848 (ppt90) REVERT: A 524 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: B 175 ASP cc_start: 0.9105 (p0) cc_final: 0.8866 (p0) REVERT: B 176 LYS cc_start: 0.9566 (mmtp) cc_final: 0.9242 (mmmm) REVERT: B 304 LYS cc_start: 0.8876 (tppp) cc_final: 0.8618 (tppp) REVERT: C 90 LEU cc_start: 0.9201 (mt) cc_final: 0.8950 (mp) REVERT: C 213 MET cc_start: 0.8429 (tpt) cc_final: 0.8061 (tpp) REVERT: C 225 MET cc_start: 0.8698 (tmm) cc_final: 0.8434 (tmm) REVERT: D 172 LYS cc_start: 0.9268 (ptmm) cc_final: 0.8888 (tmtt) REVERT: D 356 MET cc_start: 0.8974 (ttt) cc_final: 0.8466 (ttt) REVERT: E 110 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9097 (mm-30) REVERT: E 111 MET cc_start: 0.9468 (mmm) cc_final: 0.9005 (mmm) REVERT: E 194 HIS cc_start: 0.8989 (t70) cc_final: 0.8728 (t70) REVERT: E 201 LYS cc_start: 0.9631 (tppt) cc_final: 0.9334 (mmtm) REVERT: E 213 HIS cc_start: 0.9086 (m90) cc_final: 0.8675 (m90) REVERT: E 292 MET cc_start: 0.9287 (mmm) cc_final: 0.9015 (mmm) REVERT: F 17 GLU cc_start: 0.9173 (tp30) cc_final: 0.8909 (tp30) REVERT: F 68 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8285 (ppp) REVERT: F 75 MET cc_start: 0.9690 (mmm) cc_final: 0.8982 (tpp) REVERT: F 116 MET cc_start: 0.8572 (ttm) cc_final: 0.6675 (ttm) REVERT: F 125 GLN cc_start: 0.9173 (tt0) cc_final: 0.8780 (tm-30) REVERT: F 199 MET cc_start: 0.9208 (tmm) cc_final: 0.8972 (tpp) REVERT: G 1 MET cc_start: 0.8992 (tpp) cc_final: 0.8792 (tpp) REVERT: G 38 GLN cc_start: 0.8950 (tt0) cc_final: 0.8475 (tt0) REVERT: G 49 GLN cc_start: 0.8533 (tm-30) cc_final: 0.7942 (tm-30) REVERT: G 57 PHE cc_start: 0.8620 (m-80) cc_final: 0.8048 (t80) REVERT: G 211 TYR cc_start: 0.9088 (m-80) cc_final: 0.8843 (m-80) REVERT: H 1 MET cc_start: 0.9116 (tpt) cc_final: 0.8793 (tpp) REVERT: H 61 ARG cc_start: 0.9164 (ppt170) cc_final: 0.8819 (ptm160) REVERT: H 91 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.8342 (mmm-85) REVERT: H 149 ARG cc_start: 0.9216 (ttp-110) cc_final: 0.8827 (ttp-110) REVERT: H 153 HIS cc_start: 0.9319 (m170) cc_final: 0.8942 (m-70) REVERT: H 214 PHE cc_start: 0.9319 (m-10) cc_final: 0.8942 (m-80) outliers start: 40 outliers final: 30 residues processed: 229 average time/residue: 0.1601 time to fit residues: 55.5000 Evaluate side-chains 223 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 160 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 298 ASN D 345 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.082492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.056058 restraints weight = 75175.377| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 5.00 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20085 Z= 0.151 Angle : 0.637 10.548 27164 Z= 0.316 Chirality : 0.042 0.197 3170 Planarity : 0.004 0.058 3456 Dihedral : 7.092 141.217 2803 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 1.51 % Allowed : 14.07 % Favored : 84.42 % 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: 2464 helix: 1.60 (0.15), residues: 1163 sheet: -0.16 (0.22), residues: 495 loop : -0.29 (0.24), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 210 TYR 0.039 0.002 TYR B 279 PHE 0.031 0.001 PHE G 215 TRP 0.012 0.001 TRP F 28 HIS 0.004 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00333 (20085) covalent geometry : angle 0.63663 (27164) hydrogen bonds : bond 0.03444 ( 1076) hydrogen bonds : angle 4.72111 ( 3063) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7935 (t70) cc_final: 0.7671 (t-170) REVERT: A 473 ARG cc_start: 0.9133 (ptt90) cc_final: 0.8831 (ppt90) REVERT: A 524 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: B 175 ASP cc_start: 0.9095 (p0) cc_final: 0.8878 (p0) REVERT: B 176 LYS cc_start: 0.9566 (mmtp) cc_final: 0.9235 (mmmm) REVERT: B 304 LYS cc_start: 0.8860 (tppp) cc_final: 0.8630 (tppp) REVERT: B 308 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8266 (ppp) REVERT: C 90 LEU cc_start: 0.9224 (mt) cc_final: 0.8982 (mp) REVERT: C 213 MET cc_start: 0.8437 (tpt) cc_final: 0.8015 (tpp) REVERT: C 225 MET cc_start: 0.8712 (tmm) cc_final: 0.8448 (tmm) REVERT: D 172 LYS cc_start: 0.9268 (ptmm) cc_final: 0.8887 (tmtt) REVERT: D 229 TYR cc_start: 0.8986 (t80) cc_final: 0.8537 (t80) REVERT: D 356 MET cc_start: 0.8968 (ttt) cc_final: 0.8375 (ttt) REVERT: E 110 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9100 (mm-30) REVERT: E 111 MET cc_start: 0.9475 (mmm) cc_final: 0.9009 (mmm) REVERT: E 194 HIS cc_start: 0.9002 (t70) cc_final: 0.8745 (t70) REVERT: E 201 LYS cc_start: 0.9637 (tppt) cc_final: 0.9341 (mmtm) REVERT: E 213 HIS cc_start: 0.9085 (m90) cc_final: 0.8678 (m90) REVERT: F 17 GLU cc_start: 0.9183 (tp30) cc_final: 0.8883 (tp30) REVERT: F 68 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8267 (ppp) REVERT: F 75 MET cc_start: 0.9686 (mmm) cc_final: 0.8991 (tpp) REVERT: F 116 MET cc_start: 0.8576 (ttm) cc_final: 0.6686 (ttm) REVERT: F 125 GLN cc_start: 0.9248 (tt0) cc_final: 0.8843 (tm-30) REVERT: F 199 MET cc_start: 0.9209 (tmm) cc_final: 0.8965 (tpp) REVERT: F 249 TYR cc_start: 0.9085 (m-80) cc_final: 0.8860 (m-80) REVERT: G 1 MET cc_start: 0.8994 (tpp) cc_final: 0.8305 (tpp) REVERT: G 38 GLN cc_start: 0.8919 (tt0) cc_final: 0.8440 (tt0) REVERT: G 49 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7901 (tm-30) REVERT: G 57 PHE cc_start: 0.8616 (m-80) cc_final: 0.8079 (t80) REVERT: H 1 MET cc_start: 0.9077 (tpt) cc_final: 0.8800 (tpp) REVERT: H 61 ARG cc_start: 0.9151 (ppt170) cc_final: 0.8798 (ptm160) REVERT: H 91 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.8404 (mmm-85) REVERT: H 149 ARG cc_start: 0.9213 (ttp-110) cc_final: 0.8812 (ttp-110) REVERT: H 153 HIS cc_start: 0.9320 (m170) cc_final: 0.8940 (m-70) REVERT: H 214 PHE cc_start: 0.9334 (m-10) cc_final: 0.8959 (m-80) outliers start: 33 outliers final: 28 residues processed: 226 average time/residue: 0.1561 time to fit residues: 53.2195 Evaluate side-chains 223 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 232 optimal weight: 0.0030 chunk 200 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.082736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056234 restraints weight = 75979.062| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.99 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20085 Z= 0.152 Angle : 0.654 11.096 27164 Z= 0.321 Chirality : 0.042 0.191 3170 Planarity : 0.004 0.058 3456 Dihedral : 7.052 140.385 2803 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 1.46 % Allowed : 14.39 % Favored : 84.15 % 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 (0.18), residues: 2464 helix: 1.64 (0.15), residues: 1162 sheet: -0.16 (0.22), residues: 496 loop : -0.31 (0.24), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 210 TYR 0.040 0.002 TYR B 279 PHE 0.025 0.001 PHE G 215 TRP 0.010 0.001 TRP F 28 HIS 0.009 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00334 (20085) covalent geometry : angle 0.65383 (27164) hydrogen bonds : bond 0.03393 ( 1076) hydrogen bonds : angle 4.69773 ( 3063) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 HIS cc_start: 0.7965 (t70) cc_final: 0.7700 (t-170) REVERT: A 473 ARG cc_start: 0.9133 (ptt90) cc_final: 0.8823 (ppt90) REVERT: A 524 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: B 175 ASP cc_start: 0.9103 (p0) cc_final: 0.8888 (p0) REVERT: B 176 LYS cc_start: 0.9573 (mmtp) cc_final: 0.9250 (mmmm) REVERT: B 304 LYS cc_start: 0.8869 (tppp) cc_final: 0.8636 (tppp) REVERT: B 308 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8271 (ppp) REVERT: C 90 LEU cc_start: 0.9233 (mt) cc_final: 0.8995 (mp) REVERT: C 213 MET cc_start: 0.8431 (tpt) cc_final: 0.8008 (tpp) REVERT: C 225 MET cc_start: 0.8717 (tmm) cc_final: 0.8452 (tmm) REVERT: D 172 LYS cc_start: 0.9264 (ptmm) cc_final: 0.8877 (tmtt) REVERT: D 356 MET cc_start: 0.8978 (ttt) cc_final: 0.8361 (ttt) REVERT: E 110 GLU cc_start: 0.9501 (mm-30) cc_final: 0.9092 (mm-30) REVERT: E 111 MET cc_start: 0.9454 (mmm) cc_final: 0.8973 (mmm) REVERT: E 194 HIS cc_start: 0.9003 (t70) cc_final: 0.8762 (t70) REVERT: E 201 LYS cc_start: 0.9635 (tppt) cc_final: 0.9342 (mmtm) REVERT: E 213 HIS cc_start: 0.9079 (m90) cc_final: 0.8698 (m90) REVERT: F 17 GLU cc_start: 0.9175 (tp30) cc_final: 0.8866 (tp30) REVERT: F 68 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8267 (ppp) REVERT: F 75 MET cc_start: 0.9686 (mmm) cc_final: 0.8993 (tpp) REVERT: F 116 MET cc_start: 0.8611 (ttm) cc_final: 0.6736 (ttm) REVERT: F 125 GLN cc_start: 0.9346 (tt0) cc_final: 0.8885 (tm-30) REVERT: F 199 MET cc_start: 0.9209 (tmm) cc_final: 0.8936 (tpp) REVERT: G 1 MET cc_start: 0.8989 (tpp) cc_final: 0.8295 (tpp) REVERT: G 38 GLN cc_start: 0.8924 (tt0) cc_final: 0.8444 (tt0) REVERT: G 49 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7931 (tm-30) REVERT: G 57 PHE cc_start: 0.8628 (m-80) cc_final: 0.8051 (t80) REVERT: H 1 MET cc_start: 0.9063 (tpt) cc_final: 0.8817 (tpp) REVERT: H 61 ARG cc_start: 0.9159 (ppt170) cc_final: 0.8809 (ptm160) REVERT: H 91 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8420 (mmm-85) REVERT: H 149 ARG cc_start: 0.9221 (ttp-110) cc_final: 0.8819 (ttp-110) REVERT: H 153 HIS cc_start: 0.9341 (m170) cc_final: 0.8981 (m-70) REVERT: H 156 ASP cc_start: 0.9502 (p0) cc_final: 0.9267 (p0) REVERT: H 214 PHE cc_start: 0.9328 (m-10) cc_final: 0.8975 (m-80) REVERT: H 244 MET cc_start: 0.8862 (tmm) cc_final: 0.8480 (tmm) outliers start: 32 outliers final: 28 residues processed: 220 average time/residue: 0.1668 time to fit residues: 55.0200 Evaluate side-chains 225 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 68 MET Chi-restraints excluded: chain H residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 13 optimal weight: 30.0000 chunk 179 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 HIS B 298 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** H 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.082021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055411 restraints weight = 76397.424| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 5.03 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20085 Z= 0.203 Angle : 0.666 11.129 27164 Z= 0.328 Chirality : 0.042 0.188 3170 Planarity : 0.004 0.057 3456 Dihedral : 7.054 140.314 2803 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.18 % Favored : 95.78 % Rotamer: Outliers : 1.42 % Allowed : 14.57 % Favored : 84.01 % 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: 0.85 (0.18), residues: 2464 helix: 1.61 (0.15), residues: 1163 sheet: -0.19 (0.22), residues: 495 loop : -0.36 (0.24), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 210 TYR 0.040 0.002 TYR B 279 PHE 0.029 0.001 PHE G 215 TRP 0.010 0.001 TRP F 28 HIS 0.008 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00440 (20085) covalent geometry : angle 0.66611 (27164) hydrogen bonds : bond 0.03461 ( 1076) hydrogen bonds : angle 4.73446 ( 3063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3891.36 seconds wall clock time: 67 minutes 59.40 seconds (4079.40 seconds total)