Starting phenix.real_space_refine on Sun Aug 24 09:53:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifg_35416/08_2025/8ifg_35416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifg_35416/08_2025/8ifg_35416.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 { model { file = "/net/cci-nas-00/data/ceres_data/8ifg_35416/08_2025/8ifg_35416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifg_35416/08_2025/8ifg_35416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ifg_35416/08_2025/8ifg_35416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifg_35416/08_2025/8ifg_35416.map" } 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= 0.034 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 90 5.16 5 C 12194 2.51 5 N 3231 2.21 5 O 3550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 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: 19068 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3090 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 20, 'TRANS': 365} Chain breaks: 1 Chain: "A" Number of atoms: 7260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 7260 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 38, 'TRANS': 840} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2963 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain: "E" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1466 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 165} Chain: "D" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1401 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain: "F" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 963 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1921 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 220} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17672 SG CYS P 409 54.060 83.689 97.270 1.00 47.49 S ATOM 17700 SG CYS P 412 52.131 86.871 98.203 1.00 47.46 S ATOM 17890 SG CYS P 436 51.939 83.793 100.479 1.00 44.28 S ATOM 17793 SG CYS P 425 59.486 73.584 93.279 1.00 49.78 S ATOM 17819 SG CYS P 428 57.657 74.703 90.406 1.00 49.86 S ATOM 18026 SG CYS P 453 55.722 74.006 93.391 1.00 46.67 S Time building chain proxies: 4.85, per 1000 atoms: 0.25 Number of scatterers: 19068 At special positions: 0 Unit cell: (97.52, 144.16, 191.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 90 16.00 O 3550 8.00 N 3231 7.00 C 12194 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: 1.81 Conformation dependent library (CDL) restraints added in 837.7 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 175 " pdb=" ZN P 701 " pdb="ZN ZN P 701 " - pdb=" ND1 HIS P 433 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 412 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 409 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 436 " pdb=" ZN P 702 " pdb="ZN ZN P 702 " - pdb=" NE2 HIS P 456 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 453 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 428 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 425 " Number of angles added : 6 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 15 sheets defined 50.1% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'B' and resid 18 through 40 Proline residue: B 38 - end of helix Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 221 through 225 removed outlier: 4.003A pdb=" N VAL B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 225' Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.526A pdb=" N ALA B 269 " --> pdb=" O ARG B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.915A pdb=" N GLN B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 417 Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 53 through 69 removed outlier: 3.672A pdb=" N TYR A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 4.570A pdb=" N LEU A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 156 removed outlier: 3.879A pdb=" N THR A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 174 removed outlier: 4.135A pdb=" N GLN A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 191 Processing helix chain 'A' and resid 194 through 201 Processing helix chain 'A' and resid 202 through 210 Proline residue: A 206 - end of helix removed outlier: 3.814A pdb=" N ILE A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 210 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 270 through 287 Processing helix chain 'A' and resid 290 through 303 removed outlier: 4.553A pdb=" N GLY A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 Processing helix chain 'A' and resid 319 through 331 removed outlier: 4.868A pdb=" N ASN A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N SER A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.855A pdb=" N ASN A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.582A pdb=" N ILE A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 427 Processing helix chain 'A' and resid 428 through 435 Processing helix chain 'A' and resid 445 through 458 removed outlier: 4.532A pdb=" N TYR A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 472 removed outlier: 4.309A pdb=" N GLU A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 515 Proline residue: A 478 - end of helix Proline residue: A 500 - end of helix removed outlier: 4.929A pdb=" N ASP A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 514 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 521 through 530 removed outlier: 4.663A pdb=" N LYS A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 549 Processing helix chain 'A' and resid 565 through 584 Processing helix chain 'A' and resid 587 through 604 removed outlier: 4.758A pdb=" N LEU A 599 " --> pdb=" O PHE A 595 " (cutoff:3.500A) Proline residue: A 600 - end of helix Processing helix chain 'A' and resid 606 through 619 removed outlier: 4.533A pdb=" N VAL A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 746 through 768 removed outlier: 3.793A pdb=" N PHE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 780 removed outlier: 3.762A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 790 Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.513A pdb=" N LEU A 799 " --> pdb=" O TRP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 822 Processing helix chain 'A' and resid 825 through 838 Processing helix chain 'A' and resid 846 through 864 Processing helix chain 'A' and resid 866 through 876 Processing helix chain 'A' and resid 932 through 937 Processing helix chain 'A' and resid 940 through 948 Processing helix chain 'A' and resid 976 through 988 removed outlier: 3.909A pdb=" N VAL A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A 981 " --> pdb=" O GLU A 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 19 removed outlier: 3.805A pdb=" N TYR C 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 4.080A pdb=" N ARG C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 removed outlier: 4.508A pdb=" N LYS C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'C' and resid 102 through 124 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.540A pdb=" N GLY C 216 " --> pdb=" O ILE C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 249 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 274 through 287 removed outlier: 4.319A pdb=" N CYS C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL C 282 " --> pdb=" O HIS C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 318 Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 352 through 369 Processing helix chain 'E' and resid 175 through 192 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 221 through 247 removed outlier: 5.380A pdb=" N GLY E 244 " --> pdb=" O ASN E 240 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASN E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET E 246 " --> pdb=" O CYS E 242 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 263 removed outlier: 4.205A pdb=" N GLN E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN E 255 " --> pdb=" O PHE E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 Processing helix chain 'E' and resid 273 through 275 No H-bonds generated for 'chain 'E' and resid 273 through 275' Processing helix chain 'E' and resid 276 through 291 removed outlier: 3.988A pdb=" N LEU E 280 " --> pdb=" O HIS E 276 " (cutoff:3.500A) Proline residue: E 285 - end of helix Processing helix chain 'E' and resid 294 through 315 Processing helix chain 'E' and resid 315 through 320 Processing helix chain 'E' and resid 328 through 336 Processing helix chain 'D' and resid 175 through 191 Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'D' and resid 221 through 247 removed outlier: 5.819A pdb=" N GLY D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASN D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET D 246 " --> pdb=" O CYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 263 Processing helix chain 'D' and resid 267 through 272 Processing helix chain 'D' and resid 273 through 291 removed outlier: 4.138A pdb=" N ARG D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Proline residue: D 285 - end of helix removed outlier: 3.644A pdb=" N ARG D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 315 Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'F' and resid 196 through 200 removed outlier: 3.838A pdb=" N ASP F 199 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 367 removed outlier: 3.815A pdb=" N LYS F 367 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 391 Processing helix chain 'P' and resid 334 through 348 Processing helix chain 'P' and resid 356 through 363 removed outlier: 4.520A pdb=" N PHE P 363 " --> pdb=" O ILE P 359 " (cutoff:3.500A) Processing helix chain 'P' and resid 456 through 460 removed outlier: 3.890A pdb=" N HIS P 459 " --> pdb=" O HIS P 456 " (cutoff:3.500A) Processing helix chain 'P' and resid 520 through 545 Processing helix chain 'P' and resid 547 through 554 removed outlier: 3.650A pdb=" N ARG P 554 " --> pdb=" O PHE P 550 " (cutoff:3.500A) Processing helix chain 'P' and resid 557 through 565 Processing helix chain 'P' and resid 569 through 584 Processing sheet with id=AA1, first strand: chain 'B' and resid 41 through 48 removed outlier: 6.392A pdb=" N THR B 411 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE B 44 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 409 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 46 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU B 407 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 387 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 65 removed outlier: 6.368A pdb=" N GLY B 78 " --> pdb=" O MET B 54 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B 56 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE B 76 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP B 58 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS B 74 " --> pdb=" O TRP B 58 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N GLU B 72 " --> pdb=" O PRO B 60 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N GLN B 62 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 11.929A pdb=" N TYR B 70 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR B 86 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER B 127 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU B 88 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 125 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 137 Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.578A pdb=" N GLY B 203 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 190 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 201 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TRP B 192 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR B 199 " --> pdb=" O TRP B 192 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ASP B 213 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU B 226 " --> pdb=" O ASP B 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 237 through 242 removed outlier: 6.464A pdb=" N VAL B 253 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL B 240 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA B 251 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE B 242 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU B 249 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 286 through 290 removed outlier: 11.663A pdb=" N SER B 286 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N LEU B 297 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N ALA B 288 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N PHE B 295 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASN B 290 " --> pdb=" O ASN B 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.689A pdb=" N ASP B 354 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU B 374 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 343 Processing sheet with id=AB1, first strand: chain 'A' and resid 559 through 562 removed outlier: 4.959A pdb=" N LEU A 905 " --> pdb=" O MET A 922 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 741 " --> pdb=" O TRP A 910 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 49 through 51 removed outlier: 6.754A pdb=" N VAL C 254 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL C 295 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU C 256 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 168 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLN C 257 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 170 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL C 167 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N CYS C 193 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR C 169 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE C 195 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP C 171 " --> pdb=" O PHE C 195 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N LYS C 197 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL C 221 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR C 192 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL C 223 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER C 194 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 225 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS C 196 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 194 through 195 removed outlier: 3.536A pdb=" N GLN E 325 " --> pdb=" O LEU E 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 194 through 195 Processing sheet with id=AB5, first strand: chain 'P' and resid 473 through 474 removed outlier: 6.242A pdb=" N TYR F 340 " --> pdb=" O ILE P 489 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 423 through 424 856 hydrogen bonds defined for protein. 2469 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: 3.43 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4148 1.33 - 1.45: 4463 1.45 - 1.57: 10803 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 19542 Sorted by residual: bond pdb=" N PRO F 176 " pdb=" CA PRO F 176 " ideal model delta sigma weight residual 1.469 1.700 -0.231 1.28e-02 6.10e+03 3.27e+02 bond pdb=" C HIS F 175 " pdb=" N PRO F 176 " ideal model delta sigma weight residual 1.334 1.451 -0.118 2.34e-02 1.83e+03 2.52e+01 bond pdb=" CA SER F 181 " pdb=" CB SER F 181 " ideal model delta sigma weight residual 1.532 1.476 0.056 1.74e-02 3.30e+03 1.02e+01 bond pdb=" CA GLU C 14 " pdb=" C GLU C 14 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.34e-02 5.57e+03 9.38e+00 bond pdb=" N ILE E 288 " pdb=" CA ILE E 288 " ideal model delta sigma weight residual 1.461 1.491 -0.031 1.19e-02 7.06e+03 6.70e+00 ... (remaining 19537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 26389 3.95 - 7.91: 98 7.91 - 11.86: 7 11.86 - 15.81: 0 15.81 - 19.77: 1 Bond angle restraints: 26495 Sorted by residual: angle pdb=" C HIS F 175 " pdb=" N PRO F 176 " pdb=" CA PRO F 176 " ideal model delta sigma weight residual 119.84 139.61 -19.77 1.25e+00 6.40e-01 2.50e+02 angle pdb=" CA PRO F 176 " pdb=" N PRO F 176 " pdb=" CD PRO F 176 " ideal model delta sigma weight residual 112.00 100.15 11.85 1.40e+00 5.10e-01 7.16e+01 angle pdb=" N PRO F 332 " pdb=" CA PRO F 332 " pdb=" CB PRO F 332 " ideal model delta sigma weight residual 103.00 110.67 -7.67 1.10e+00 8.26e-01 4.87e+01 angle pdb=" N PRO P 514 " pdb=" CA PRO P 514 " pdb=" CB PRO P 514 " ideal model delta sigma weight residual 103.25 110.44 -7.19 1.05e+00 9.07e-01 4.69e+01 angle pdb=" C THR E 291 " pdb=" N ASN E 292 " pdb=" CA ASN E 292 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 ... (remaining 26490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10275 17.98 - 35.95: 1124 35.95 - 53.93: 264 53.93 - 71.91: 55 71.91 - 89.88: 29 Dihedral angle restraints: 11747 sinusoidal: 4822 harmonic: 6925 Sorted by residual: dihedral pdb=" CA PHE A 98 " pdb=" C PHE A 98 " pdb=" N LEU A 99 " pdb=" CA LEU A 99 " ideal model delta harmonic sigma weight residual 180.00 119.59 60.41 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA VAL A 72 " pdb=" C VAL A 72 " pdb=" N ASP A 73 " pdb=" CA ASP A 73 " ideal model delta harmonic sigma weight residual 180.00 146.53 33.47 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA ALA P 597 " pdb=" C ALA P 597 " pdb=" N PRO P 598 " pdb=" CA PRO P 598 " ideal model delta harmonic sigma weight residual 180.00 147.79 32.21 0 5.00e+00 4.00e-02 4.15e+01 ... (remaining 11744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2180 0.051 - 0.101: 566 0.101 - 0.152: 120 0.152 - 0.203: 3 0.203 - 0.253: 4 Chirality restraints: 2873 Sorted by residual: chirality pdb=" CA PRO F 176 " pdb=" N PRO F 176 " pdb=" C PRO F 176 " pdb=" CB PRO F 176 " both_signs ideal model delta sigma weight residual False 2.72 2.97 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE F 167 " pdb=" CA ILE F 167 " pdb=" CG1 ILE F 167 " pdb=" CG2 ILE F 167 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA PRO F 332 " pdb=" N PRO F 332 " pdb=" C PRO F 332 " pdb=" CB PRO F 332 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2870 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 374 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.77e+00 pdb=" N PRO F 375 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 375 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 375 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA P 597 " -0.048 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO P 598 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO P 598 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO P 598 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 99 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO A 100 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " 0.038 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 284 2.62 - 3.19: 17480 3.19 - 3.76: 29725 3.76 - 4.33: 40364 4.33 - 4.90: 65012 Nonbonded interactions: 152865 Sorted by model distance: nonbonded pdb=" OD1 ASP C 173 " pdb="ZN ZN C 501 " model vdw 2.044 2.230 nonbonded pdb=" OD2 ASP C 261 " pdb="ZN ZN C 501 " model vdw 2.053 2.230 nonbonded pdb=" O TYR B 394 " pdb=" OG1 THR B 397 " model vdw 2.124 3.040 nonbonded pdb=" NH1 ARG E 250 " pdb=" O GLY F 211 " model vdw 2.173 3.120 nonbonded pdb=" O LEU A 997 " pdb=" OG1 THR A1014 " model vdw 2.174 3.040 ... (remaining 152860 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 'D' selection = (chain 'E' and resid 170 through 337) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.140 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 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 : 0.007 0.297 19551 Z= 0.312 Angle : 0.750 19.766 26501 Z= 0.430 Chirality : 0.047 0.253 2873 Planarity : 0.006 0.074 3416 Dihedral : 16.266 89.885 7259 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.36 % Favored : 91.46 % Rotamer: Outliers : 5.26 % Allowed : 12.73 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.09 % 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: -2.83 (0.16), residues: 2308 helix: -0.65 (0.14), residues: 1038 sheet: -1.68 (0.31), residues: 247 loop : -3.31 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 471 TYR 0.020 0.002 TYR C 10 PHE 0.021 0.002 PHE A 74 TRP 0.022 0.002 TRP F 180 HIS 0.007 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00612 (19542) covalent geometry : angle 0.74634 (26495) hydrogen bonds : bond 0.11239 ( 856) hydrogen bonds : angle 5.21109 ( 2469) metal coordination : bond 0.13397 ( 9) metal coordination : angle 4.64216 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 382 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.7248 (tppt) cc_final: 0.6631 (ttmt) REVERT: B 278 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.6030 (t70) REVERT: A 117 GLN cc_start: 0.7686 (tp40) cc_final: 0.7353 (tm-30) REVERT: A 141 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7401 (p) REVERT: A 162 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.6162 (tp40) REVERT: A 173 PHE cc_start: 0.7635 (t80) cc_final: 0.7378 (t80) REVERT: A 508 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8000 (ttmt) REVERT: A 527 LYS cc_start: 0.7649 (mptt) cc_final: 0.7381 (mptt) REVERT: A 815 MET cc_start: 0.8529 (mmm) cc_final: 0.7833 (mmt) REVERT: C 47 LYS cc_start: 0.7616 (mmtt) cc_final: 0.6970 (mmmt) REVERT: C 165 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7945 (tp40) REVERT: C 369 ASN cc_start: 0.8623 (t0) cc_final: 0.8401 (t0) REVERT: E 164 GLU cc_start: 0.4508 (OUTLIER) cc_final: 0.1107 (pt0) REVERT: D 252 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8160 (mt-10) REVERT: F 174 LYS cc_start: 0.6956 (mttt) cc_final: 0.6663 (mmtt) REVERT: F 182 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6925 (tp40) REVERT: F 370 GLU cc_start: 0.8443 (mp0) cc_final: 0.7680 (mt-10) outliers start: 112 outliers final: 57 residues processed: 470 average time/residue: 0.1628 time to fit residues: 115.1909 Evaluate side-chains 326 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 264 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 182 GLN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 352 GLN Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain P residue 484 LYS Chi-restraints excluded: chain P residue 486 ASN Chi-restraints excluded: chain P residue 491 GLU Chi-restraints excluded: chain P residue 519 PHE Chi-restraints excluded: chain P residue 527 VAL Chi-restraints excluded: chain P residue 534 VAL Chi-restraints excluded: chain P residue 551 TYR Chi-restraints excluded: chain P residue 560 LEU Chi-restraints excluded: chain P residue 572 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 30.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 280 HIS ** B 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN ** B 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN A 255 ASN A 282 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 548 HIS A 724 HIS A 767 GLN A 789 GLN A 797 ASN A 860 HIS A 876 GLN A 912 ASN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** C 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS C 164 HIS C 222 ASN C 247 GLN E 218 HIS E 230 GLN E 326 ASN D 261 GLN D 303 ASN D 326 ASN F 182 GLN F 191 ASN ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 438 ASN P 568 ASN P 593 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.209993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122249 restraints weight = 21611.319| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.05 r_work: 0.3343 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19551 Z= 0.209 Angle : 0.692 10.276 26501 Z= 0.355 Chirality : 0.045 0.193 2873 Planarity : 0.006 0.076 3416 Dihedral : 8.838 77.057 2677 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.32 % Favored : 92.50 % Rotamer: Outliers : 4.23 % Allowed : 16.39 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.09 % 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: -1.58 (0.17), residues: 2308 helix: 0.69 (0.16), residues: 1029 sheet: -1.67 (0.30), residues: 267 loop : -2.83 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 200 TYR 0.026 0.002 TYR A 105 PHE 0.021 0.002 PHE C 147 TRP 0.020 0.002 TRP F 180 HIS 0.007 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00507 (19542) covalent geometry : angle 0.69195 (26495) hydrogen bonds : bond 0.05147 ( 856) hydrogen bonds : angle 4.59206 ( 2469) metal coordination : bond 0.01064 ( 9) metal coordination : angle 1.40816 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 275 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 GLU cc_start: 0.5305 (OUTLIER) cc_final: 0.4162 (pm20) REVERT: B 79 VAL cc_start: 0.6045 (OUTLIER) cc_final: 0.5812 (p) REVERT: B 137 LEU cc_start: 0.8319 (mm) cc_final: 0.7899 (pt) REVERT: A 61 MET cc_start: 0.8344 (mmt) cc_final: 0.7867 (mmp) REVERT: A 117 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: A 141 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7341 (t) REVERT: A 162 GLN cc_start: 0.6096 (OUTLIER) cc_final: 0.5844 (tp40) REVERT: A 485 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 508 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7509 (ttmt) REVERT: A 527 LYS cc_start: 0.7671 (mptt) cc_final: 0.7217 (mptt) REVERT: A 549 PHE cc_start: 0.8000 (m-80) cc_final: 0.7770 (m-10) REVERT: A 795 ARG cc_start: 0.7590 (ttm170) cc_final: 0.7313 (mtm-85) REVERT: A 815 MET cc_start: 0.8116 (mmm) cc_final: 0.7606 (mmt) REVERT: C 47 LYS cc_start: 0.7214 (mmtt) cc_final: 0.6812 (mtpp) REVERT: C 165 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8380 (tp40) REVERT: C 171 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8018 (t0) REVERT: E 246 MET cc_start: 0.8684 (ptp) cc_final: 0.8415 (ptp) REVERT: D 251 PHE cc_start: 0.8965 (t80) cc_final: 0.8758 (t80) REVERT: D 303 ASN cc_start: 0.8376 (m-40) cc_final: 0.7948 (t0) REVERT: F 365 GLU cc_start: 0.8390 (tt0) cc_final: 0.8042 (tp30) REVERT: F 370 GLU cc_start: 0.8540 (mp0) cc_final: 0.8247 (mt-10) REVERT: F 372 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6239 (pm20) REVERT: P 469 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7553 (mmtt) REVERT: P 474 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7281 (ptm-80) REVERT: P 489 ILE cc_start: 0.8273 (tp) cc_final: 0.8027 (tp) REVERT: P 563 LEU cc_start: 0.7964 (mm) cc_final: 0.7760 (mm) outliers start: 90 outliers final: 52 residues processed: 346 average time/residue: 0.1648 time to fit residues: 86.0895 Evaluate side-chains 307 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 247 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 474 ARG Chi-restraints excluded: chain P residue 484 LYS Chi-restraints excluded: chain P residue 486 ASN Chi-restraints excluded: chain P residue 519 PHE Chi-restraints excluded: chain P residue 537 ASP Chi-restraints excluded: chain P residue 551 TYR Chi-restraints excluded: chain P residue 560 LEU Chi-restraints excluded: chain P residue 572 GLU Chi-restraints excluded: chain P residue 585 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 92 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 GLN B 378 HIS ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN A 602 HIS A 860 HIS A 950 GLN C 20 HIS D 254 GLN ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.220608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.140766 restraints weight = 21988.862| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 3.07 r_work: 0.3587 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19551 Z= 0.175 Angle : 0.642 9.973 26501 Z= 0.326 Chirality : 0.043 0.236 2873 Planarity : 0.006 0.079 3416 Dihedral : 7.757 78.182 2622 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.93 % Favored : 92.98 % Rotamer: Outliers : 4.13 % Allowed : 17.71 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.09 % 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: -1.11 (0.18), residues: 2308 helix: 1.12 (0.16), residues: 1028 sheet: -1.59 (0.30), residues: 269 loop : -2.57 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 982 TYR 0.018 0.001 TYR F 204 PHE 0.016 0.001 PHE C 147 TRP 0.013 0.001 TRP B 390 HIS 0.007 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00421 (19542) covalent geometry : angle 0.64166 (26495) hydrogen bonds : bond 0.04751 ( 856) hydrogen bonds : angle 4.45659 ( 2469) metal coordination : bond 0.00643 ( 9) metal coordination : angle 1.30289 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 247 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: B 50 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.4173 (pm20) REVERT: B 56 LEU cc_start: 0.8034 (pt) cc_final: 0.7672 (pp) REVERT: B 79 VAL cc_start: 0.6367 (OUTLIER) cc_final: 0.6118 (p) REVERT: B 347 ASP cc_start: 0.6820 (p0) cc_final: 0.5701 (t0) REVERT: B 387 ASP cc_start: 0.5706 (t0) cc_final: 0.5443 (t0) REVERT: A 61 MET cc_start: 0.8526 (mmt) cc_final: 0.7998 (mmp) REVERT: A 91 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7671 (mm) REVERT: A 117 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: A 141 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7638 (t) REVERT: A 527 LYS cc_start: 0.8141 (mptt) cc_final: 0.7719 (mptt) REVERT: A 595 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7431 (t80) REVERT: C 24 GLN cc_start: 0.8499 (mp10) cc_final: 0.8175 (mm-40) REVERT: C 47 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7231 (mtpp) REVERT: C 165 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8316 (tp40) REVERT: C 171 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7788 (t0) REVERT: E 246 MET cc_start: 0.8849 (ptp) cc_final: 0.8630 (ptp) REVERT: E 290 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.7387 (ttm-80) REVERT: D 315 HIS cc_start: 0.7450 (m90) cc_final: 0.7124 (m-70) REVERT: F 370 GLU cc_start: 0.8692 (mp0) cc_final: 0.8384 (mt-10) REVERT: F 372 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6557 (pm20) REVERT: P 469 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7557 (mmtt) REVERT: P 474 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7538 (ptm-80) REVERT: P 489 ILE cc_start: 0.8303 (tp) cc_final: 0.8037 (tp) REVERT: P 563 LEU cc_start: 0.8127 (mm) cc_final: 0.7710 (mm) REVERT: P 572 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6590 (tp30) outliers start: 88 outliers final: 54 residues processed: 317 average time/residue: 0.1602 time to fit residues: 76.8096 Evaluate side-chains 303 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 239 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain P residue 352 GLN Chi-restraints excluded: chain P residue 474 ARG Chi-restraints excluded: chain P residue 484 LYS Chi-restraints excluded: chain P residue 486 ASN Chi-restraints excluded: chain P residue 534 VAL Chi-restraints excluded: chain P residue 551 TYR Chi-restraints excluded: chain P residue 560 LEU Chi-restraints excluded: chain P residue 572 GLU Chi-restraints excluded: chain P residue 585 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 1 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 16 optimal weight: 50.0000 chunk 94 optimal weight: 0.0270 chunk 208 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 194 optimal weight: 0.0970 chunk 134 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS C 18 ASN C 30 HIS C 87 HIS D 255 GLN F 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.225143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.141398 restraints weight = 21604.922| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.82 r_work: 0.3654 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19551 Z= 0.109 Angle : 0.575 9.960 26501 Z= 0.291 Chirality : 0.041 0.167 2873 Planarity : 0.005 0.079 3416 Dihedral : 7.200 79.700 2614 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.94 % Favored : 94.02 % Rotamer: Outliers : 3.10 % Allowed : 19.40 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.70 (0.18), residues: 2308 helix: 1.51 (0.17), residues: 1032 sheet: -1.38 (0.31), residues: 250 loop : -2.42 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 449 TYR 0.016 0.001 TYR F 204 PHE 0.019 0.001 PHE A 594 TRP 0.013 0.001 TRP B 390 HIS 0.006 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00236 (19542) covalent geometry : angle 0.57501 (26495) hydrogen bonds : bond 0.03777 ( 856) hydrogen bonds : angle 4.25436 ( 2469) metal coordination : bond 0.00399 ( 9) metal coordination : angle 0.93897 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 248 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LEU cc_start: 0.8053 (pt) cc_final: 0.7717 (pp) REVERT: B 75 MET cc_start: 0.7248 (mmt) cc_final: 0.6958 (mmt) REVERT: B 347 ASP cc_start: 0.6602 (p0) cc_final: 0.5574 (t0) REVERT: B 387 ASP cc_start: 0.5753 (t0) cc_final: 0.5492 (t0) REVERT: A 61 MET cc_start: 0.8468 (mmt) cc_final: 0.8045 (mmp) REVERT: A 141 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7214 (p) REVERT: A 310 ARG cc_start: 0.7313 (mtt180) cc_final: 0.6909 (mtt-85) REVERT: A 485 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 527 LYS cc_start: 0.8025 (mptt) cc_final: 0.7569 (mptt) REVERT: C 24 GLN cc_start: 0.8442 (mp10) cc_final: 0.8086 (mm-40) REVERT: C 47 LYS cc_start: 0.7501 (mmtt) cc_final: 0.7071 (mtpp) REVERT: C 81 MET cc_start: 0.6026 (ttt) cc_final: 0.5799 (tmm) REVERT: C 165 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8238 (tp40) REVERT: C 312 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7210 (mt-10) REVERT: D 315 HIS cc_start: 0.7209 (m90) cc_final: 0.6862 (m-70) REVERT: F 364 ASN cc_start: 0.8165 (t0) cc_final: 0.7908 (t0) REVERT: P 469 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7533 (mmtt) REVERT: P 474 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7517 (ptm-80) REVERT: P 489 ILE cc_start: 0.8100 (tp) cc_final: 0.7870 (tp) REVERT: P 563 LEU cc_start: 0.8084 (mm) cc_final: 0.7826 (mm) outliers start: 66 outliers final: 44 residues processed: 297 average time/residue: 0.1618 time to fit residues: 72.9091 Evaluate side-chains 283 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain P residue 352 GLN Chi-restraints excluded: chain P residue 474 ARG Chi-restraints excluded: chain P residue 484 LYS Chi-restraints excluded: chain P residue 486 ASN Chi-restraints excluded: chain P residue 551 TYR Chi-restraints excluded: chain P residue 572 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN C 88 GLN ** F 390 ASN ** 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 = 0.4623 r_free = 0.4623 target = 0.221472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136660 restraints weight = 21558.561| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.77 r_work: 0.3599 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19551 Z= 0.158 Angle : 0.610 13.080 26501 Z= 0.308 Chirality : 0.042 0.249 2873 Planarity : 0.005 0.077 3416 Dihedral : 6.603 56.537 2598 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.50 % Favored : 93.46 % Rotamer: Outliers : 3.43 % Allowed : 20.29 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.09 % 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: -0.63 (0.18), residues: 2308 helix: 1.51 (0.17), residues: 1037 sheet: -1.33 (0.31), residues: 255 loop : -2.33 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 449 TYR 0.019 0.001 TYR P 344 PHE 0.013 0.001 PHE A 594 TRP 0.013 0.001 TRP B 390 HIS 0.005 0.001 HIS P 433 Details of bonding type rmsd covalent geometry : bond 0.00381 (19542) covalent geometry : angle 0.60958 (26495) hydrogen bonds : bond 0.04381 ( 856) hydrogen bonds : angle 4.30353 ( 2469) metal coordination : bond 0.00569 ( 9) metal coordination : angle 1.35681 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 236 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: B 56 LEU cc_start: 0.8133 (pt) cc_final: 0.7847 (pp) REVERT: B 387 ASP cc_start: 0.5893 (t0) cc_final: 0.5508 (t70) REVERT: A 61 MET cc_start: 0.8540 (mmt) cc_final: 0.7740 (mmp) REVERT: A 91 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7618 (mm) REVERT: A 117 GLN cc_start: 0.8121 (tp40) cc_final: 0.7330 (tm-30) REVERT: A 141 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7648 (t) REVERT: A 168 ASP cc_start: 0.7207 (m-30) cc_final: 0.6948 (m-30) REVERT: A 485 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7485 (mt-10) REVERT: A 527 LYS cc_start: 0.8156 (mptt) cc_final: 0.7414 (mmtt) REVERT: A 815 MET cc_start: 0.8467 (mmm) cc_final: 0.7639 (mmt) REVERT: C 24 GLN cc_start: 0.8508 (mp10) cc_final: 0.8145 (mm-40) REVERT: C 47 LYS cc_start: 0.7591 (mmtt) cc_final: 0.7166 (mtpp) REVERT: C 81 MET cc_start: 0.6053 (ttt) cc_final: 0.5800 (tmm) REVERT: C 171 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7732 (t0) REVERT: E 252 GLU cc_start: 0.8269 (pm20) cc_final: 0.7868 (pm20) REVERT: D 315 HIS cc_start: 0.7268 (m90) cc_final: 0.6872 (m-70) REVERT: P 469 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7566 (mmtt) REVERT: P 474 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7549 (ptm-80) REVERT: P 489 ILE cc_start: 0.8165 (tp) cc_final: 0.7954 (tp) REVERT: P 563 LEU cc_start: 0.8107 (mm) cc_final: 0.7815 (mm) REVERT: P 572 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6374 (tt0) outliers start: 73 outliers final: 50 residues processed: 293 average time/residue: 0.1652 time to fit residues: 73.0572 Evaluate side-chains 283 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain P residue 352 GLN Chi-restraints excluded: chain P residue 474 ARG Chi-restraints excluded: chain P residue 484 LYS Chi-restraints excluded: chain P residue 486 ASN Chi-restraints excluded: chain P residue 534 VAL Chi-restraints excluded: chain P residue 543 GLU Chi-restraints excluded: chain P residue 551 TYR Chi-restraints excluded: chain P residue 572 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 114 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 219 optimal weight: 0.0470 chunk 87 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 HIS ** A 978 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 = 0.4632 r_free = 0.4632 target = 0.222675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.138033 restraints weight = 21451.040| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.79 r_work: 0.3617 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19551 Z= 0.133 Angle : 0.592 14.343 26501 Z= 0.297 Chirality : 0.041 0.213 2873 Planarity : 0.005 0.079 3416 Dihedral : 6.417 56.055 2597 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.15 % Favored : 93.80 % Rotamer: Outliers : 3.57 % Allowed : 20.48 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.09 % 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: -0.50 (0.18), residues: 2308 helix: 1.60 (0.16), residues: 1039 sheet: -1.31 (0.31), residues: 250 loop : -2.24 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 449 TYR 0.014 0.001 TYR F 204 PHE 0.012 0.001 PHE E 308 TRP 0.013 0.001 TRP B 390 HIS 0.003 0.001 HIS P 433 Details of bonding type rmsd covalent geometry : bond 0.00312 (19542) covalent geometry : angle 0.59150 (26495) hydrogen bonds : bond 0.04071 ( 856) hydrogen bonds : angle 4.24865 ( 2469) metal coordination : bond 0.00480 ( 9) metal coordination : angle 1.23486 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 234 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: B 56 LEU cc_start: 0.8146 (pt) cc_final: 0.7805 (pp) REVERT: B 138 MET cc_start: 0.7434 (mmm) cc_final: 0.7013 (mmm) REVERT: B 255 TYR cc_start: 0.5989 (OUTLIER) cc_final: 0.5781 (t80) REVERT: B 387 ASP cc_start: 0.5920 (t0) cc_final: 0.5538 (t0) REVERT: A 61 MET cc_start: 0.8555 (mmt) cc_final: 0.7682 (mmp) REVERT: A 141 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7528 (t) REVERT: A 485 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7478 (mt-10) REVERT: A 527 LYS cc_start: 0.8106 (mptt) cc_final: 0.7392 (mmtt) REVERT: C 24 GLN cc_start: 0.8450 (mp10) cc_final: 0.8074 (mm-40) REVERT: C 47 LYS cc_start: 0.7601 (mmtt) cc_final: 0.7189 (mtpp) REVERT: C 81 MET cc_start: 0.6126 (ttt) cc_final: 0.5721 (tmm) REVERT: C 171 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7681 (t0) REVERT: E 252 GLU cc_start: 0.8280 (pm20) cc_final: 0.7909 (pm20) REVERT: D 315 HIS cc_start: 0.7194 (m90) cc_final: 0.6793 (m-70) REVERT: P 469 LYS cc_start: 0.7797 (mmtt) cc_final: 0.7529 (mmtt) REVERT: P 474 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7530 (ptm-80) REVERT: P 489 ILE cc_start: 0.8143 (tp) cc_final: 0.7882 (tp) outliers start: 76 outliers final: 56 residues processed: 292 average time/residue: 0.1614 time to fit residues: 71.3905 Evaluate side-chains 288 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 228 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 255 TYR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain P residue 352 GLN Chi-restraints excluded: chain P residue 474 ARG Chi-restraints excluded: chain P residue 484 LYS Chi-restraints excluded: chain P residue 486 ASN Chi-restraints excluded: chain P residue 534 VAL Chi-restraints excluded: chain P residue 551 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 28 optimal weight: 40.0000 chunk 129 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 390 ASN ** 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 = 0.4618 r_free = 0.4618 target = 0.220987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.136169 restraints weight = 21554.680| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.77 r_work: 0.3596 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19551 Z= 0.159 Angle : 0.617 13.348 26501 Z= 0.308 Chirality : 0.042 0.281 2873 Planarity : 0.005 0.077 3416 Dihedral : 6.383 54.963 2593 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.54 % Favored : 93.41 % Rotamer: Outliers : 3.19 % Allowed : 21.18 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.09 % 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: -0.51 (0.18), residues: 2308 helix: 1.56 (0.16), residues: 1038 sheet: -1.40 (0.32), residues: 240 loop : -2.16 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 310 TYR 0.013 0.001 TYR C 334 PHE 0.013 0.001 PHE E 308 TRP 0.009 0.001 TRP F 180 HIS 0.004 0.001 HIS P 433 Details of bonding type rmsd covalent geometry : bond 0.00383 (19542) covalent geometry : angle 0.61676 (26495) hydrogen bonds : bond 0.04355 ( 856) hydrogen bonds : angle 4.29259 ( 2469) metal coordination : bond 0.00580 ( 9) metal coordination : angle 1.42253 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 232 time to evaluate : 0.795 Fit side-chains REVERT: B 56 LEU cc_start: 0.8198 (pt) cc_final: 0.7843 (pp) REVERT: B 137 LEU cc_start: 0.7436 (pt) cc_final: 0.7083 (mm) REVERT: B 377 MET cc_start: 0.6395 (ptm) cc_final: 0.6091 (ttt) REVERT: B 387 ASP cc_start: 0.5949 (t0) cc_final: 0.5552 (t0) REVERT: A 37 LEU cc_start: 0.8045 (mt) cc_final: 0.7811 (mm) REVERT: A 61 MET cc_start: 0.8548 (mmt) cc_final: 0.7759 (mmp) REVERT: A 117 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: A 141 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7654 (t) REVERT: A 527 LYS cc_start: 0.8171 (mptt) cc_final: 0.7389 (tptp) REVERT: A 540 ILE cc_start: 0.8325 (tp) cc_final: 0.8040 (tp) REVERT: C 24 GLN cc_start: 0.8446 (mp10) cc_final: 0.8070 (mm-40) REVERT: C 47 LYS cc_start: 0.7642 (mmtt) cc_final: 0.7217 (mtpp) REVERT: C 81 MET cc_start: 0.6096 (ttt) cc_final: 0.5752 (tmm) REVERT: C 123 SER cc_start: 0.8705 (t) cc_final: 0.8491 (t) REVERT: E 252 GLU cc_start: 0.8281 (pm20) cc_final: 0.7746 (pm20) REVERT: D 293 MET cc_start: 0.4712 (tmm) cc_final: 0.4214 (tmm) REVERT: D 315 HIS cc_start: 0.7214 (m90) cc_final: 0.6793 (m-70) REVERT: P 469 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7494 (mmtt) REVERT: P 474 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7532 (ptm-80) REVERT: P 489 ILE cc_start: 0.8185 (tp) cc_final: 0.7967 (tp) outliers start: 68 outliers final: 57 residues processed: 285 average time/residue: 0.1611 time to fit residues: 69.8524 Evaluate side-chains 288 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 228 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 255 GLN Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain P residue 352 GLN Chi-restraints excluded: chain P residue 474 ARG Chi-restraints excluded: chain P residue 484 LYS Chi-restraints excluded: chain P residue 486 ASN Chi-restraints excluded: chain P residue 534 VAL Chi-restraints excluded: chain P residue 543 GLU Chi-restraints excluded: chain P residue 551 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 93 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 220 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 13 optimal weight: 40.0000 chunk 122 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.220750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.135888 restraints weight = 21627.966| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.79 r_work: 0.3593 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19551 Z= 0.162 Angle : 0.618 15.785 26501 Z= 0.310 Chirality : 0.043 0.269 2873 Planarity : 0.005 0.078 3416 Dihedral : 6.393 53.423 2593 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.41 % Favored : 93.54 % Rotamer: Outliers : 3.33 % Allowed : 21.47 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.18), residues: 2308 helix: 1.64 (0.16), residues: 1034 sheet: -1.42 (0.32), residues: 240 loop : -2.12 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 75 TYR 0.013 0.001 TYR P 551 PHE 0.013 0.001 PHE E 308 TRP 0.013 0.001 TRP B 192 HIS 0.005 0.001 HIS P 433 Details of bonding type rmsd covalent geometry : bond 0.00391 (19542) covalent geometry : angle 0.61750 (26495) hydrogen bonds : bond 0.04400 ( 856) hydrogen bonds : angle 4.30725 ( 2469) metal coordination : bond 0.00609 ( 9) metal coordination : angle 1.47710 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 235 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LEU cc_start: 0.8180 (pt) cc_final: 0.7783 (pp) REVERT: B 137 LEU cc_start: 0.7372 (pt) cc_final: 0.7160 (mm) REVERT: B 387 ASP cc_start: 0.5924 (t0) cc_final: 0.5428 (t70) REVERT: A 37 LEU cc_start: 0.8048 (mt) cc_final: 0.7819 (mm) REVERT: A 61 MET cc_start: 0.8553 (mmt) cc_final: 0.7760 (mmp) REVERT: A 91 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7573 (mm) REVERT: A 117 GLN cc_start: 0.8100 (tp40) cc_final: 0.6816 (tm-30) REVERT: A 141 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7639 (t) REVERT: A 485 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7512 (mt-10) REVERT: A 527 LYS cc_start: 0.8135 (mptt) cc_final: 0.7354 (tptp) REVERT: A 540 ILE cc_start: 0.8315 (tp) cc_final: 0.8024 (tp) REVERT: A 571 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: C 24 GLN cc_start: 0.8438 (mp10) cc_final: 0.8055 (mm-40) REVERT: C 47 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7136 (mtpp) REVERT: C 81 MET cc_start: 0.6100 (ttt) cc_final: 0.5772 (tmm) REVERT: C 123 SER cc_start: 0.8754 (t) cc_final: 0.8550 (t) REVERT: C 171 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7726 (t0) REVERT: E 252 GLU cc_start: 0.8292 (pm20) cc_final: 0.7810 (pm20) REVERT: E 290 ARG cc_start: 0.7645 (ttm-80) cc_final: 0.7329 (ttm-80) REVERT: E 291 THR cc_start: 0.8511 (t) cc_final: 0.8172 (t) REVERT: D 293 MET cc_start: 0.4534 (tmm) cc_final: 0.4154 (tmm) REVERT: D 315 HIS cc_start: 0.7205 (m90) cc_final: 0.6790 (m-70) REVERT: P 469 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7415 (mmtt) REVERT: P 474 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7534 (ptm-80) REVERT: P 489 ILE cc_start: 0.8202 (tp) cc_final: 0.7996 (tp) outliers start: 71 outliers final: 58 residues processed: 289 average time/residue: 0.1547 time to fit residues: 67.9445 Evaluate side-chains 294 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 231 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain P residue 352 GLN Chi-restraints excluded: chain P residue 474 ARG Chi-restraints excluded: chain P residue 484 LYS Chi-restraints excluded: chain P residue 486 ASN Chi-restraints excluded: chain P residue 534 VAL Chi-restraints excluded: chain P residue 543 GLU Chi-restraints excluded: chain P residue 551 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 225 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 HIS ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 ASN ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 390 ASN ** 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 = 0.4586 r_free = 0.4586 target = 0.216633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.131626 restraints weight = 21592.755| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.74 r_work: 0.3543 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19551 Z= 0.246 Angle : 0.690 10.266 26501 Z= 0.349 Chirality : 0.045 0.264 2873 Planarity : 0.006 0.076 3416 Dihedral : 6.680 54.575 2593 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.11 % Favored : 92.85 % Rotamer: Outliers : 3.15 % Allowed : 21.75 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.09 % 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: -0.63 (0.18), residues: 2308 helix: 1.35 (0.16), residues: 1040 sheet: -1.43 (0.32), residues: 244 loop : -2.11 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 369 TYR 0.019 0.002 TYR P 551 PHE 0.018 0.002 PHE E 308 TRP 0.011 0.001 TRP B 212 HIS 0.006 0.001 HIS P 433 Details of bonding type rmsd covalent geometry : bond 0.00610 (19542) covalent geometry : angle 0.68978 (26495) hydrogen bonds : bond 0.05267 ( 856) hydrogen bonds : angle 4.49000 ( 2469) metal coordination : bond 0.00888 ( 9) metal coordination : angle 2.10522 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LEU cc_start: 0.8050 (pt) cc_final: 0.7551 (pp) REVERT: B 137 LEU cc_start: 0.7488 (pt) cc_final: 0.7198 (mm) REVERT: B 387 ASP cc_start: 0.5994 (t0) cc_final: 0.5507 (t70) REVERT: A 37 LEU cc_start: 0.8075 (mt) cc_final: 0.7826 (mm) REVERT: A 61 MET cc_start: 0.8594 (mmt) cc_final: 0.8023 (mmp) REVERT: A 141 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7696 (p) REVERT: A 527 LYS cc_start: 0.8292 (mptt) cc_final: 0.7443 (tptp) REVERT: A 540 ILE cc_start: 0.8339 (tp) cc_final: 0.8025 (tp) REVERT: A 571 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: C 24 GLN cc_start: 0.8450 (mp10) cc_final: 0.8079 (mm-40) REVERT: C 47 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7259 (mtpp) REVERT: C 81 MET cc_start: 0.6094 (ttt) cc_final: 0.5677 (tmm) REVERT: C 312 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7496 (mt-10) REVERT: E 252 GLU cc_start: 0.8302 (pm20) cc_final: 0.7864 (pm20) REVERT: E 290 ARG cc_start: 0.7667 (ttm-80) cc_final: 0.7335 (ttm-80) REVERT: E 291 THR cc_start: 0.8659 (t) cc_final: 0.8388 (t) REVERT: D 293 MET cc_start: 0.4691 (tmm) cc_final: 0.4200 (tmm) REVERT: D 303 ASN cc_start: 0.8512 (m-40) cc_final: 0.8002 (t0) REVERT: D 315 HIS cc_start: 0.7407 (m90) cc_final: 0.7184 (m90) REVERT: P 474 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7583 (ptm-80) outliers start: 67 outliers final: 55 residues processed: 303 average time/residue: 0.1565 time to fit residues: 72.3261 Evaluate side-chains 298 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 240 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain P residue 474 ARG Chi-restraints excluded: chain P residue 484 LYS Chi-restraints excluded: chain P residue 486 ASN Chi-restraints excluded: chain P residue 534 VAL Chi-restraints excluded: chain P residue 551 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 88 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 18 optimal weight: 30.0000 chunk 128 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 51 optimal weight: 0.0030 chunk 52 optimal weight: 0.9980 chunk 225 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 HIS ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.223402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.139710 restraints weight = 21527.604| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.75 r_work: 0.3637 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19551 Z= 0.115 Angle : 0.602 16.722 26501 Z= 0.299 Chirality : 0.041 0.244 2873 Planarity : 0.005 0.081 3416 Dihedral : 6.184 53.685 2592 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.59 % Favored : 94.37 % Rotamer: Outliers : 2.35 % Allowed : 22.64 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.27 (0.18), residues: 2308 helix: 1.75 (0.16), residues: 1031 sheet: -1.32 (0.33), residues: 234 loop : -1.99 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 58 TYR 0.013 0.001 TYR F 204 PHE 0.010 0.001 PHE E 228 TRP 0.012 0.001 TRP D 181 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00259 (19542) covalent geometry : angle 0.60162 (26495) hydrogen bonds : bond 0.03786 ( 856) hydrogen bonds : angle 4.25325 ( 2469) metal coordination : bond 0.00518 ( 9) metal coordination : angle 1.27561 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: B 56 LEU cc_start: 0.8082 (pt) cc_final: 0.7664 (pp) REVERT: B 137 LEU cc_start: 0.7324 (pt) cc_final: 0.7122 (mm) REVERT: B 200 LEU cc_start: 0.4800 (tt) cc_final: 0.4588 (tp) REVERT: B 387 ASP cc_start: 0.6000 (t0) cc_final: 0.5526 (t70) REVERT: A 37 LEU cc_start: 0.8066 (mt) cc_final: 0.7825 (mm) REVERT: A 61 MET cc_start: 0.8568 (mmt) cc_final: 0.8246 (mmp) REVERT: A 91 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7735 (mm) REVERT: A 118 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.6998 (t80) REVERT: A 141 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7385 (p) REVERT: A 485 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 527 LYS cc_start: 0.8196 (mptt) cc_final: 0.7368 (tptp) REVERT: A 540 ILE cc_start: 0.8286 (tp) cc_final: 0.8029 (tp) REVERT: A 609 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7064 (ptmm) REVERT: C 24 GLN cc_start: 0.8402 (mp10) cc_final: 0.8002 (mm-40) REVERT: C 47 LYS cc_start: 0.7586 (mmtt) cc_final: 0.7148 (mtpp) REVERT: C 81 MET cc_start: 0.6069 (ttt) cc_final: 0.5757 (tmm) REVERT: C 171 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7632 (t0) REVERT: E 252 GLU cc_start: 0.8276 (pm20) cc_final: 0.7871 (pm20) REVERT: E 290 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7284 (ttm-80) REVERT: D 315 HIS cc_start: 0.7245 (m90) cc_final: 0.6873 (m-70) REVERT: F 364 ASN cc_start: 0.8204 (t0) cc_final: 0.7940 (t0) REVERT: P 474 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7525 (ptm-80) REVERT: P 484 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.6428 (tppt) outliers start: 50 outliers final: 41 residues processed: 276 average time/residue: 0.1552 time to fit residues: 65.2672 Evaluate side-chains 276 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain P residue 352 GLN Chi-restraints excluded: chain P residue 474 ARG Chi-restraints excluded: chain P residue 484 LYS Chi-restraints excluded: chain P residue 486 ASN Chi-restraints excluded: chain P residue 534 VAL Chi-restraints excluded: chain P residue 551 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 17 optimal weight: 50.0000 chunk 198 optimal weight: 8.9990 chunk 98 optimal weight: 0.0670 chunk 196 optimal weight: 2.9990 chunk 123 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 119 optimal weight: 0.0470 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN A 602 HIS A 978 GLN E 255 GLN F 175 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.214582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127373 restraints weight = 21842.516| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.09 r_work: 0.3415 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19551 Z= 0.115 Angle : 0.600 16.497 26501 Z= 0.298 Chirality : 0.041 0.237 2873 Planarity : 0.005 0.077 3416 Dihedral : 5.954 53.750 2590 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.02 % Favored : 93.93 % Rotamer: Outliers : 2.58 % Allowed : 22.78 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.15 (0.18), residues: 2308 helix: 1.85 (0.16), residues: 1034 sheet: -1.33 (0.33), residues: 234 loop : -1.92 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 58 TYR 0.012 0.001 TYR F 204 PHE 0.012 0.001 PHE E 228 TRP 0.015 0.001 TRP B 192 HIS 0.003 0.001 HIS P 433 Details of bonding type rmsd covalent geometry : bond 0.00263 (19542) covalent geometry : angle 0.59947 (26495) hydrogen bonds : bond 0.03721 ( 856) hydrogen bonds : angle 4.20952 ( 2469) metal coordination : bond 0.00389 ( 9) metal coordination : angle 1.09260 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5850.94 seconds wall clock time: 101 minutes 3.49 seconds (6063.49 seconds total)