Starting phenix.real_space_refine on Mon May 19 19:49:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifg_35416/05_2025/8ifg_35416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifg_35416/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ifg_35416/05_2025/8ifg_35416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifg_35416/05_2025/8ifg_35416.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifg_35416/05_2025/8ifg_35416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifg_35416/05_2025/8ifg_35416.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 1, 'TRP: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: 9.74, per 1000 atoms: 0.51 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: 4.61 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.09 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: 6.63 Time building geometry restraints manager: 5.33 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 44.440 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.520 ------------------------------------------------------------------------------- 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 : 13.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.002 TRP F 180 HIS 0.007 0.001 HIS C 30 PHE 0.021 0.002 PHE A 74 TYR 0.020 0.002 TYR C 10 ARG 0.006 0.000 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.11239 ( 856) hydrogen bonds : angle 5.21109 ( 2469) metal coordination : bond 0.13397 ( 9) metal coordination : angle 4.64216 ( 6) covalent geometry : bond 0.00612 (19542) covalent geometry : angle 0.74634 (26495) *********************** 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 : 2.218 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: 0.6031 (t70) REVERT: A 117 GLN cc_start: 0.7686 (tp40) cc_final: 0.7352 (tm-30) REVERT: A 141 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7402 (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: A 966 LEU cc_start: 0.8736 (mt) cc_final: 0.8532 (mp) 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: 0.7944 (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: 0.1110 (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: 58 residues processed: 470 average time/residue: 0.3116 time to fit residues: 218.8653 Evaluate side-chains 327 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 264 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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 355 LEU 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 194 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 chunk 93 optimal weight: 0.4980 chunk 180 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 208 optimal weight: 30.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN 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 912 ASN A 950 GLN A 969 ASN C 18 ASN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 P 438 ASN P 568 ASN P 593 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.216235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129852 restraints weight = 21425.858| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.09 r_work: 0.3431 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19551 Z= 0.135 Angle : 0.633 9.558 26501 Z= 0.324 Chirality : 0.042 0.189 2873 Planarity : 0.006 0.073 3416 Dihedral : 8.681 78.138 2679 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.46 % Favored : 93.41 % Rotamer: Outliers : 3.48 % Allowed : 16.67 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.17), residues: 2308 helix: 0.83 (0.16), residues: 1032 sheet: -1.58 (0.31), residues: 257 loop : -2.83 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 390 HIS 0.006 0.001 HIS A 860 PHE 0.017 0.001 PHE C 147 TYR 0.024 0.001 TYR A 105 ARG 0.006 0.000 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 856) hydrogen bonds : angle 4.45309 ( 2469) metal coordination : bond 0.01020 ( 9) metal coordination : angle 0.45836 ( 6) covalent geometry : bond 0.00303 (19542) covalent geometry : angle 0.63312 (26495) *********************** 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 352 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 278 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 GLU cc_start: 0.5360 (OUTLIER) cc_final: 0.4096 (pm20) REVERT: B 79 VAL cc_start: 0.6171 (OUTLIER) cc_final: 0.5958 (p) REVERT: B 137 LEU cc_start: 0.8240 (mm) cc_final: 0.7824 (pt) REVERT: B 377 MET cc_start: 0.7552 (ttt) cc_final: 0.7047 (ttt) REVERT: A 61 MET cc_start: 0.8146 (mmt) cc_final: 0.7602 (mmp) REVERT: A 117 GLN cc_start: 0.7511 (tp40) cc_final: 0.6851 (tm-30) REVERT: A 141 THR cc_start: 0.7345 (OUTLIER) cc_final: 0.6903 (p) REVERT: A 451 LYS cc_start: 0.7312 (ttpt) cc_final: 0.7100 (ptmt) REVERT: A 508 LYS cc_start: 0.7987 (ttmt) cc_final: 0.7425 (ttmt) REVERT: A 527 LYS cc_start: 0.7377 (mptt) cc_final: 0.6907 (mptt) REVERT: A 549 PHE cc_start: 0.7950 (m-80) cc_final: 0.7711 (m-10) REVERT: A 768 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.8145 (mtm110) REVERT: A 795 ARG cc_start: 0.7480 (ttm170) cc_final: 0.7035 (mtt180) REVERT: A 815 MET cc_start: 0.8238 (mmm) cc_final: 0.7518 (mmt) REVERT: C 47 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6603 (mtpp) REVERT: C 165 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8456 (tp40) REVERT: C 365 GLU cc_start: 0.7883 (tp30) cc_final: 0.7584 (mm-30) REVERT: D 268 MET cc_start: 0.8046 (mmp) cc_final: 0.7776 (mmt) REVERT: D 315 HIS cc_start: 0.7069 (m-70) cc_final: 0.6797 (m-70) REVERT: F 365 GLU cc_start: 0.8461 (tt0) cc_final: 0.8135 (tp30) REVERT: P 474 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7154 (ptm-80) REVERT: P 489 ILE cc_start: 0.8187 (tp) cc_final: 0.7879 (tp) outliers start: 74 outliers final: 42 residues processed: 334 average time/residue: 0.3201 time to fit residues: 160.6197 Evaluate side-chains 294 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 2.260 ------------------------------------------------------------------------------- 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 84 ILE 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 455 LEU Chi-restraints excluded: chain A residue 463 GLU 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 862 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain E residue 170 HIS Chi-restraints excluded: chain E residue 290 ARG 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 474 ARG 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 551 TYR Chi-restraints excluded: chain P residue 572 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 48 optimal weight: 0.2980 chunk 162 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 378 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS A 876 GLN C 30 HIS C 88 GLN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS P 536 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.216627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.130099 restraints weight = 21379.137| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.09 r_work: 0.3438 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19551 Z= 0.120 Angle : 0.585 9.261 26501 Z= 0.297 Chirality : 0.041 0.229 2873 Planarity : 0.005 0.075 3416 Dihedral : 7.437 79.611 2617 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.89 % Favored : 94.02 % Rotamer: Outliers : 3.90 % Allowed : 17.33 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.18), residues: 2308 helix: 1.40 (0.16), residues: 1029 sheet: -1.49 (0.31), residues: 258 loop : -2.58 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 390 HIS 0.007 0.001 HIS B 336 PHE 0.018 0.001 PHE A 594 TYR 0.020 0.001 TYR D 331 ARG 0.005 0.000 ARG A 982 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 856) hydrogen bonds : angle 4.26688 ( 2469) metal coordination : bond 0.00386 ( 9) metal coordination : angle 0.79601 ( 6) covalent geometry : bond 0.00268 (19542) covalent geometry : angle 0.58506 (26495) *********************** 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 345 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 262 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 SER cc_start: 0.7039 (t) cc_final: 0.6807 (t) REVERT: B 347 ASP cc_start: 0.6423 (p0) cc_final: 0.5396 (t0) REVERT: B 377 MET cc_start: 0.7716 (ttt) cc_final: 0.7099 (ttt) REVERT: B 387 ASP cc_start: 0.5259 (t0) cc_final: 0.4725 (t0) REVERT: A 61 MET cc_start: 0.8272 (mmt) cc_final: 0.7887 (mmp) REVERT: A 141 THR cc_start: 0.7339 (OUTLIER) cc_final: 0.6877 (p) REVERT: A 485 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 508 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7443 (ttmt) REVERT: A 527 LYS cc_start: 0.7626 (mptt) cc_final: 0.7132 (mptt) REVERT: A 768 ARG cc_start: 0.8546 (ttp-170) cc_final: 0.8164 (mtm110) REVERT: A 795 ARG cc_start: 0.7536 (ttm170) cc_final: 0.7087 (mtt180) REVERT: A 815 MET cc_start: 0.8213 (mmm) cc_final: 0.7488 (mmt) REVERT: A 982 ARG cc_start: 0.6782 (ttm-80) cc_final: 0.6541 (tpp80) REVERT: C 24 GLN cc_start: 0.8508 (mp10) cc_final: 0.8062 (mm-40) REVERT: C 47 LYS cc_start: 0.7215 (mmtt) cc_final: 0.6827 (mtpp) REVERT: C 81 MET cc_start: 0.5904 (ttt) cc_final: 0.5541 (tmm) REVERT: C 165 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8433 (tp40) REVERT: C 319 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7565 (mt-10) REVERT: E 290 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.7030 (ttm-80) REVERT: E 293 MET cc_start: 0.8451 (mtp) cc_final: 0.8211 (mtp) REVERT: F 365 GLU cc_start: 0.8332 (tt0) cc_final: 0.7942 (tp30) REVERT: F 372 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6153 (pm20) REVERT: P 474 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7209 (ptm-80) REVERT: P 489 ILE cc_start: 0.8122 (tp) cc_final: 0.7795 (tp) outliers start: 83 outliers final: 44 residues processed: 325 average time/residue: 0.3189 time to fit residues: 154.9134 Evaluate side-chains 286 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 156 LEU 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 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 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 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 50 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 340 LEU Chi-restraints excluded: chain E residue 255 GLN 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 178 SER 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 491 GLU Chi-restraints excluded: chain P residue 551 TYR Chi-restraints excluded: chain P residue 572 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 192 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 173 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 362 GLN B 378 HIS ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS C 20 HIS C 87 HIS C 137 HIS ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.213107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125279 restraints weight = 21604.134| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.07 r_work: 0.3386 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19551 Z= 0.157 Angle : 0.613 10.504 26501 Z= 0.309 Chirality : 0.042 0.184 2873 Planarity : 0.005 0.073 3416 Dihedral : 6.955 59.787 2602 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.85 % Favored : 93.11 % Rotamer: Outliers : 3.57 % Allowed : 18.37 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 2308 helix: 1.46 (0.16), residues: 1031 sheet: -1.35 (0.31), residues: 261 loop : -2.40 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 180 HIS 0.008 0.001 HIS B 378 PHE 0.018 0.001 PHE D 251 TYR 0.016 0.001 TYR F 204 ARG 0.004 0.000 ARG A 982 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 856) hydrogen bonds : angle 4.30638 ( 2469) metal coordination : bond 0.00552 ( 9) metal coordination : angle 1.07464 ( 6) covalent geometry : bond 0.00372 (19542) covalent geometry : angle 0.61244 (26495) *********************** 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 325 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 249 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 347 ASP cc_start: 0.6288 (p0) cc_final: 0.5345 (t0) REVERT: B 377 MET cc_start: 0.7868 (ttt) cc_final: 0.7205 (ttt) REVERT: B 387 ASP cc_start: 0.5090 (t0) cc_final: 0.4789 (t0) REVERT: A 61 MET cc_start: 0.8329 (mmt) cc_final: 0.7544 (mmp) REVERT: A 117 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: A 141 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7217 (t) REVERT: A 485 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7219 (mt-10) REVERT: A 527 LYS cc_start: 0.7561 (mptt) cc_final: 0.7072 (mptt) REVERT: C 24 GLN cc_start: 0.8589 (mp10) cc_final: 0.8131 (mm-40) REVERT: C 47 LYS cc_start: 0.7372 (mmtt) cc_final: 0.7039 (mtpp) REVERT: C 81 MET cc_start: 0.5811 (ttt) cc_final: 0.5454 (tmm) REVERT: E 290 ARG cc_start: 0.7278 (ttm-80) cc_final: 0.6990 (ttm-80) REVERT: D 306 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7942 (mm-30) REVERT: D 315 HIS cc_start: 0.6912 (m90) cc_final: 0.6547 (m-70) REVERT: F 365 GLU cc_start: 0.8297 (tt0) cc_final: 0.7907 (tp30) REVERT: P 469 LYS cc_start: 0.7493 (mmtt) cc_final: 0.7236 (mmtt) REVERT: P 474 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7275 (ptm-80) REVERT: P 489 ILE cc_start: 0.8113 (tp) cc_final: 0.7818 (tp) REVERT: P 516 LYS cc_start: 0.7408 (ttpt) cc_final: 0.7205 (tttm) outliers start: 76 outliers final: 46 residues processed: 308 average time/residue: 0.3463 time to fit residues: 165.1186 Evaluate side-chains 287 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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 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 463 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 860 HIS 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 50 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 255 GLN 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 271 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 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 491 GLU Chi-restraints excluded: chain P residue 534 VAL 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 102 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 119 optimal weight: 0.0270 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN B 362 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS D 254 GLN ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.211877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131080 restraints weight = 21470.860| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.73 r_work: 0.3363 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2929 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= 0.159 Angle : 0.613 14.086 26501 Z= 0.308 Chirality : 0.042 0.250 2873 Planarity : 0.005 0.075 3416 Dihedral : 6.699 57.923 2597 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.50 % Favored : 93.46 % Rotamer: Outliers : 3.01 % Allowed : 19.59 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2308 helix: 1.50 (0.16), residues: 1032 sheet: -1.28 (0.31), residues: 255 loop : -2.30 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 180 HIS 0.016 0.001 HIS A 860 PHE 0.021 0.001 PHE A 594 TYR 0.019 0.001 TYR A 105 ARG 0.005 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 856) hydrogen bonds : angle 4.31879 ( 2469) metal coordination : bond 0.00578 ( 9) metal coordination : angle 1.30405 ( 6) covalent geometry : bond 0.00381 (19542) covalent geometry : angle 0.61232 (26495) *********************** 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 310 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 246 time to evaluate : 1.953 Fit side-chains revert: symmetry clash REVERT: B 138 MET cc_start: 0.6753 (tpt) cc_final: 0.6463 (mmm) REVERT: B 278 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.7102 (t70) REVERT: B 377 MET cc_start: 0.7622 (ttt) cc_final: 0.6972 (ttt) REVERT: B 387 ASP cc_start: 0.5092 (t0) cc_final: 0.4681 (t0) REVERT: A 61 MET cc_start: 0.8314 (mmt) cc_final: 0.7540 (mmp) REVERT: A 117 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.6458 (tm-30) REVERT: A 141 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7116 (t) REVERT: A 485 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7172 (mt-10) REVERT: A 527 LYS cc_start: 0.7458 (mptt) cc_final: 0.7000 (mptt) REVERT: C 24 GLN cc_start: 0.8510 (mp10) cc_final: 0.8019 (mm-40) REVERT: C 47 LYS cc_start: 0.7367 (mmtt) cc_final: 0.7009 (mtpp) REVERT: C 81 MET cc_start: 0.5737 (ttt) cc_final: 0.5389 (tmm) REVERT: E 290 ARG cc_start: 0.7324 (ttm-80) cc_final: 0.7035 (ttm-80) REVERT: D 306 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7780 (mm-30) REVERT: D 315 HIS cc_start: 0.6757 (m90) cc_final: 0.6388 (m-70) REVERT: F 365 GLU cc_start: 0.8194 (tt0) cc_final: 0.7796 (tp30) REVERT: P 474 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7192 (ptm-80) REVERT: P 489 ILE cc_start: 0.8133 (tp) cc_final: 0.7835 (tp) REVERT: P 572 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.5924 (tp30) outliers start: 64 outliers final: 46 residues processed: 294 average time/residue: 0.3006 time to fit residues: 134.4695 Evaluate side-chains 290 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 253 VAL Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 84 ILE 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 463 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 618 PHE 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 50 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 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 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 474 ARG 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 534 VAL 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 175 optimal weight: 0.9980 chunk 195 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 125 optimal weight: 0.5980 chunk 36 optimal weight: 30.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.213196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125975 restraints weight = 21814.162| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.05 r_work: 0.3392 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19551 Z= 0.130 Angle : 0.587 14.354 26501 Z= 0.294 Chirality : 0.041 0.206 2873 Planarity : 0.005 0.076 3416 Dihedral : 6.387 56.644 2595 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.07 % Favored : 93.89 % Rotamer: Outliers : 3.15 % Allowed : 20.10 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2308 helix: 1.62 (0.16), residues: 1038 sheet: -1.25 (0.31), residues: 256 loop : -2.23 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.003 0.001 HIS P 433 PHE 0.016 0.001 PHE A 594 TYR 0.014 0.001 TYR F 204 ARG 0.003 0.000 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 856) hydrogen bonds : angle 4.24660 ( 2469) metal coordination : bond 0.00463 ( 9) metal coordination : angle 1.17042 ( 6) covalent geometry : bond 0.00304 (19542) covalent geometry : angle 0.58675 (26495) *********************** 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 306 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 2.206 Fit side-chains revert: symmetry clash REVERT: B 138 MET cc_start: 0.6865 (tpt) cc_final: 0.6601 (mmm) REVERT: B 377 MET cc_start: 0.7651 (ttt) cc_final: 0.7009 (ttt) REVERT: B 387 ASP cc_start: 0.5126 (t0) cc_final: 0.4767 (t0) REVERT: A 61 MET cc_start: 0.8340 (mmt) cc_final: 0.8033 (mmp) REVERT: A 141 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7121 (t) REVERT: A 485 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7228 (mt-10) REVERT: A 527 LYS cc_start: 0.7680 (mptt) cc_final: 0.6949 (mmtt) REVERT: A 606 GLU cc_start: 0.6927 (tp30) cc_final: 0.5821 (mm-30) REVERT: A 609 LYS cc_start: 0.7515 (mtmm) cc_final: 0.7095 (ptmm) REVERT: C 24 GLN cc_start: 0.8491 (mp10) cc_final: 0.8009 (mm-40) REVERT: C 47 LYS cc_start: 0.7472 (mmtt) cc_final: 0.7090 (mtpp) REVERT: C 81 MET cc_start: 0.5845 (ttt) cc_final: 0.5493 (tmm) REVERT: E 252 GLU cc_start: 0.8227 (pm20) cc_final: 0.7872 (pm20) REVERT: D 290 ARG cc_start: 0.7014 (tpp80) cc_final: 0.6234 (mpt-90) REVERT: D 293 MET cc_start: 0.4351 (tmm) cc_final: 0.4135 (tmm) REVERT: D 315 HIS cc_start: 0.6766 (m90) cc_final: 0.6375 (m-70) REVERT: F 365 GLU cc_start: 0.8194 (tt0) cc_final: 0.7847 (tp30) REVERT: P 474 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7243 (ptm-80) REVERT: P 489 ILE cc_start: 0.8156 (tp) cc_final: 0.7861 (tp) REVERT: P 572 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.5811 (tt0) outliers start: 67 outliers final: 49 residues processed: 288 average time/residue: 0.3164 time to fit residues: 138.6552 Evaluate side-chains 284 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 2.060 ------------------------------------------------------------------------------- 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 327 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 84 ILE 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 463 GLU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 860 HIS 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 50 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 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 170 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 491 GLU Chi-restraints excluded: chain P residue 534 VAL Chi-restraints excluded: chain P residue 551 TYR Chi-restraints excluded: chain P residue 572 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 184 optimal weight: 8.9990 chunk 17 optimal weight: 30.0000 chunk 183 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 HIS ** B 362 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 839 ASN A 860 HIS ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.205511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117109 restraints weight = 21670.011| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.00 r_work: 0.3281 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 19551 Z= 0.307 Angle : 0.748 14.653 26501 Z= 0.378 Chirality : 0.048 0.281 2873 Planarity : 0.006 0.075 3416 Dihedral : 6.832 67.309 2594 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.58 % Favored : 92.33 % Rotamer: Outliers : 3.10 % Allowed : 21.18 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2308 helix: 1.15 (0.16), residues: 1038 sheet: -1.27 (0.32), residues: 249 loop : -2.27 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 180 HIS 0.044 0.002 HIS A 860 PHE 0.022 0.002 PHE P 519 TYR 0.022 0.002 TYR P 344 ARG 0.007 0.001 ARG E 290 Details of bonding type rmsd hydrogen bonds : bond 0.05851 ( 856) hydrogen bonds : angle 4.60679 ( 2469) metal coordination : bond 0.01057 ( 9) metal coordination : angle 2.48713 ( 6) covalent geometry : bond 0.00764 (19542) covalent geometry : angle 0.74730 (26495) *********************** 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 318 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 252 time to evaluate : 2.267 Fit side-chains REVERT: B 138 MET cc_start: 0.6890 (tpt) cc_final: 0.6499 (mmm) REVERT: B 278 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7186 (t70) REVERT: B 377 MET cc_start: 0.7692 (ttt) cc_final: 0.7054 (ttt) REVERT: B 387 ASP cc_start: 0.5038 (t0) cc_final: 0.4645 (t0) REVERT: A 37 LEU cc_start: 0.7923 (mt) cc_final: 0.7674 (mm) REVERT: A 61 MET cc_start: 0.8421 (mmt) cc_final: 0.8018 (mmp) REVERT: A 141 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7251 (p) REVERT: A 527 LYS cc_start: 0.7699 (mptt) cc_final: 0.6921 (tptp) REVERT: A 540 ILE cc_start: 0.7896 (tp) cc_final: 0.7570 (tp) REVERT: A 606 GLU cc_start: 0.6947 (tp30) cc_final: 0.5867 (mm-30) REVERT: C 24 GLN cc_start: 0.8550 (mp10) cc_final: 0.8056 (mm-40) REVERT: C 47 LYS cc_start: 0.7504 (mmtt) cc_final: 0.7111 (mtpp) REVERT: C 81 MET cc_start: 0.5815 (ttt) cc_final: 0.5422 (tmm) REVERT: E 252 GLU cc_start: 0.8210 (pm20) cc_final: 0.7706 (pm20) REVERT: E 291 THR cc_start: 0.8279 (t) cc_final: 0.8024 (t) REVERT: D 303 ASN cc_start: 0.8377 (m-40) cc_final: 0.7740 (t0) REVERT: D 315 HIS cc_start: 0.7079 (m90) cc_final: 0.6656 (m-70) REVERT: F 174 LYS cc_start: 0.6003 (mttt) cc_final: 0.5698 (mmtt) REVERT: F 365 GLU cc_start: 0.8305 (tt0) cc_final: 0.7890 (tp30) REVERT: P 474 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7287 (ptm-80) REVERT: P 489 ILE cc_start: 0.8319 (tp) cc_final: 0.8043 (tp) outliers start: 66 outliers final: 52 residues processed: 300 average time/residue: 0.3276 time to fit residues: 148.3604 Evaluate side-chains 300 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 278 HIS Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 87 ASP 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 551 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 860 HIS 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 50 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 255 GLN 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 178 SER Chi-restraints excluded: chain F residue 338 CYS 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 491 GLU Chi-restraints excluded: chain P residue 534 VAL 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 119 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 23 optimal weight: 30.0000 chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.222788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138493 restraints weight = 21614.535| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.79 r_work: 0.3619 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19551 Z= 0.123 Angle : 0.604 15.760 26501 Z= 0.302 Chirality : 0.041 0.260 2873 Planarity : 0.005 0.079 3416 Dihedral : 6.346 67.557 2591 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.94 % Favored : 94.02 % Rotamer: Outliers : 2.58 % Allowed : 21.89 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2308 helix: 1.64 (0.16), residues: 1031 sheet: -1.27 (0.32), residues: 250 loop : -2.14 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 180 HIS 0.018 0.001 HIS A 860 PHE 0.009 0.001 PHE C 238 TYR 0.021 0.001 TYR P 344 ARG 0.006 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 856) hydrogen bonds : angle 4.30006 ( 2469) metal coordination : bond 0.00541 ( 9) metal coordination : angle 1.32899 ( 6) covalent geometry : bond 0.00282 (19542) covalent geometry : angle 0.60408 (26495) *********************** 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 296 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 241 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 377 MET cc_start: 0.7890 (ttt) cc_final: 0.7231 (ttt) REVERT: B 387 ASP cc_start: 0.5537 (t0) cc_final: 0.5108 (t0) REVERT: A 37 LEU cc_start: 0.8047 (mt) cc_final: 0.7822 (mm) REVERT: A 61 MET cc_start: 0.8588 (mmt) cc_final: 0.8262 (mmp) REVERT: A 141 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7401 (p) REVERT: A 485 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 527 LYS cc_start: 0.8099 (mptt) cc_final: 0.7329 (tptp) REVERT: A 540 ILE cc_start: 0.8275 (tp) cc_final: 0.8032 (tp) REVERT: A 749 MET cc_start: 0.7654 (ttm) cc_final: 0.7413 (ttt) REVERT: C 24 GLN cc_start: 0.8418 (mp10) cc_final: 0.8032 (mm-40) REVERT: C 47 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7305 (mtpp) REVERT: C 81 MET cc_start: 0.5945 (ttt) cc_final: 0.5637 (tmm) REVERT: E 252 GLU cc_start: 0.8265 (pm20) cc_final: 0.7747 (pm20) REVERT: D 315 HIS cc_start: 0.7224 (m90) cc_final: 0.6852 (m-70) REVERT: F 174 LYS cc_start: 0.6211 (mttt) cc_final: 0.5888 (mmtt) REVERT: F 364 ASN cc_start: 0.8288 (t0) cc_final: 0.8001 (t0) REVERT: P 474 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7551 (ptm-80) REVERT: P 489 ILE cc_start: 0.8061 (tp) cc_final: 0.7800 (tp) REVERT: P 593 GLN cc_start: 0.6267 (mt0) cc_final: 0.5984 (mt0) outliers start: 55 outliers final: 49 residues processed: 282 average time/residue: 0.3095 time to fit residues: 132.1634 Evaluate side-chains 285 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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 187 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 84 ILE 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 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 551 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 860 HIS 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 50 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 205 THR Chi-restraints excluded: chain C residue 215 THR 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 170 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 474 ARG Chi-restraints excluded: chain P residue 484 LYS Chi-restraints excluded: chain P residue 491 GLU Chi-restraints excluded: chain P residue 534 VAL 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 31 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 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 860 HIS ** A 978 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 = 0.4613 r_free = 0.4613 target = 0.220588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135487 restraints weight = 21558.373| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.77 r_work: 0.3573 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3486 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= 0.166 Angle : 0.630 16.040 26501 Z= 0.315 Chirality : 0.042 0.254 2873 Planarity : 0.005 0.078 3416 Dihedral : 6.353 62.984 2589 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.80 % Favored : 93.15 % Rotamer: Outliers : 2.77 % Allowed : 21.89 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2308 helix: 1.63 (0.16), residues: 1032 sheet: -1.36 (0.32), residues: 245 loop : -2.08 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 180 HIS 0.012 0.001 HIS A 860 PHE 0.013 0.001 PHE P 519 TYR 0.022 0.001 TYR P 344 ARG 0.006 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 856) hydrogen bonds : angle 4.33563 ( 2469) metal coordination : bond 0.00619 ( 9) metal coordination : angle 1.65213 ( 6) covalent geometry : bond 0.00403 (19542) covalent geometry : angle 0.62953 (26495) *********************** 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 299 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 240 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 MET cc_start: 0.7431 (mmm) cc_final: 0.6148 (mmt) REVERT: B 377 MET cc_start: 0.7713 (ttt) cc_final: 0.7060 (ttt) REVERT: B 387 ASP cc_start: 0.5129 (t0) cc_final: 0.4713 (t0) REVERT: A 37 LEU cc_start: 0.8012 (mt) cc_final: 0.7758 (mm) REVERT: A 61 MET cc_start: 0.8502 (mmt) cc_final: 0.7606 (mmp) REVERT: A 141 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7573 (t) REVERT: A 485 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7323 (mt-10) REVERT: A 527 LYS cc_start: 0.7971 (mptt) cc_final: 0.7184 (tptp) REVERT: A 540 ILE cc_start: 0.8127 (tp) cc_final: 0.7809 (tp) REVERT: C 24 GLN cc_start: 0.8436 (mp10) cc_final: 0.8002 (mm-40) REVERT: C 47 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7325 (mtpp) REVERT: C 81 MET cc_start: 0.5888 (ttt) cc_final: 0.5571 (tmm) REVERT: E 252 GLU cc_start: 0.8298 (pm20) cc_final: 0.7793 (pm20) REVERT: E 268 MET cc_start: 0.6387 (tpp) cc_final: 0.6182 (tpp) REVERT: E 291 THR cc_start: 0.7870 (t) cc_final: 0.7466 (t) REVERT: D 293 MET cc_start: 0.4361 (tmm) cc_final: 0.3853 (tmm) REVERT: D 315 HIS cc_start: 0.7077 (m90) cc_final: 0.6669 (m-70) REVERT: F 174 LYS cc_start: 0.5963 (mttt) cc_final: 0.5678 (mmtt) REVERT: P 474 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7419 (ptm-80) REVERT: P 489 ILE cc_start: 0.8203 (tp) cc_final: 0.7975 (tp) outliers start: 59 outliers final: 50 residues processed: 284 average time/residue: 0.3169 time to fit residues: 136.1970 Evaluate side-chains 287 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 1.974 ------------------------------------------------------------------------------- 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 187 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 84 ILE 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 329 SER Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 860 HIS 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 50 VAL 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 205 THR Chi-restraints excluded: chain C residue 215 THR 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 178 SER Chi-restraints excluded: chain F residue 338 CYS 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 491 GLU 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 0 optimal weight: 30.0000 chunk 158 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 186 optimal weight: 0.0070 chunk 117 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 HIS ** B 362 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 860 HIS ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.220768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135694 restraints weight = 21489.444| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.78 r_work: 0.3591 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19551 Z= 0.162 Angle : 0.629 16.197 26501 Z= 0.314 Chirality : 0.042 0.249 2873 Planarity : 0.005 0.077 3416 Dihedral : 6.309 61.568 2589 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.67 % Favored : 93.28 % Rotamer: Outliers : 2.77 % Allowed : 22.08 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2308 helix: 1.62 (0.16), residues: 1034 sheet: -1.29 (0.32), residues: 255 loop : -2.08 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 180 HIS 0.017 0.001 HIS A 860 PHE 0.012 0.001 PHE P 519 TYR 0.022 0.001 TYR P 344 ARG 0.006 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 856) hydrogen bonds : angle 4.33987 ( 2469) metal coordination : bond 0.00633 ( 9) metal coordination : angle 1.65986 ( 6) covalent geometry : bond 0.00392 (19542) covalent geometry : angle 0.62852 (26495) ********************** 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 299 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 240 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 LEU cc_start: 0.7331 (pt) cc_final: 0.6965 (mm) REVERT: B 138 MET cc_start: 0.7072 (mmm) cc_final: 0.6204 (mmt) REVERT: B 278 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.6934 (t70) REVERT: B 377 MET cc_start: 0.7881 (ttt) cc_final: 0.7218 (ttt) REVERT: B 387 ASP cc_start: 0.5483 (t0) cc_final: 0.4993 (t0) REVERT: A 37 LEU cc_start: 0.8047 (mt) cc_final: 0.7798 (mm) REVERT: A 61 MET cc_start: 0.8548 (mmt) cc_final: 0.8209 (mmp) REVERT: A 141 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7629 (t) REVERT: A 485 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 527 LYS cc_start: 0.8129 (mptt) cc_final: 0.7355 (tptp) REVERT: A 540 ILE cc_start: 0.8306 (tp) cc_final: 0.8019 (tp) REVERT: C 24 GLN cc_start: 0.8430 (mp10) cc_final: 0.8042 (mm-40) REVERT: C 47 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7250 (mtpp) REVERT: C 81 MET cc_start: 0.5971 (ttt) cc_final: 0.5667 (tmm) REVERT: C 319 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7522 (mt-10) REVERT: E 252 GLU cc_start: 0.8298 (pm20) cc_final: 0.7789 (pm20) REVERT: E 291 THR cc_start: 0.8028 (t) cc_final: 0.7655 (t) REVERT: D 293 MET cc_start: 0.4428 (tmm) cc_final: 0.3908 (tmm) REVERT: D 315 HIS cc_start: 0.7285 (m90) cc_final: 0.6900 (m-70) REVERT: F 174 LYS cc_start: 0.6144 (mttt) cc_final: 0.5838 (mmtt) REVERT: P 474 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7538 (ptm-80) REVERT: P 489 ILE cc_start: 0.8182 (tp) cc_final: 0.7960 (tp) REVERT: P 593 GLN cc_start: 0.6443 (mt0) cc_final: 0.6136 (mt0) outliers start: 59 outliers final: 55 residues processed: 284 average time/residue: 0.3236 time to fit residues: 139.1205 Evaluate side-chains 293 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 2.175 ------------------------------------------------------------------------------- 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 187 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 84 ILE 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 329 SER Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 860 HIS 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 50 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 123 SER 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 205 THR Chi-restraints excluded: chain C residue 215 THR 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 302 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 338 CYS 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 491 GLU 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 142 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 228 optimal weight: 0.2980 chunk 100 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 HIS ** B 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.223926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139752 restraints weight = 21605.118| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.80 r_work: 0.3640 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19551 Z= 0.116 Angle : 0.595 16.555 26501 Z= 0.295 Chirality : 0.041 0.235 2873 Planarity : 0.005 0.079 3416 Dihedral : 6.074 56.214 2589 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.02 % Favored : 93.93 % Rotamer: Outliers : 2.54 % Allowed : 22.22 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2308 helix: 1.82 (0.16), residues: 1030 sheet: -1.22 (0.32), residues: 250 loop : -1.96 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 180 HIS 0.024 0.001 HIS A 860 PHE 0.009 0.001 PHE P 519 TYR 0.022 0.001 TYR P 344 ARG 0.006 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 856) hydrogen bonds : angle 4.22144 ( 2469) metal coordination : bond 0.00475 ( 9) metal coordination : angle 1.22404 ( 6) covalent geometry : bond 0.00266 (19542) covalent geometry : angle 0.59488 (26495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10725.09 seconds wall clock time: 186 minutes 30.52 seconds (11190.52 seconds total)