Starting phenix.real_space_refine on Fri Jun 5 16:51:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1f_65532/06_2026/9w1f_65532_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1f_65532/06_2026/9w1f_65532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w1f_65532/06_2026/9w1f_65532_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1f_65532/06_2026/9w1f_65532_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w1f_65532/06_2026/9w1f_65532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1f_65532/06_2026/9w1f_65532.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 24 5.49 5 Mg 6 5.21 5 S 86 5.16 5 C 13640 2.51 5 N 3964 2.21 5 O 3964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21690 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4758 Classifications: {'peptide': 607} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 565} Chain breaks: 1 Chain: "B" Number of atoms: 4754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4754 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 566} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2887 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2965 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3017 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 360} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2979 Classifications: {'peptide': 383} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 354} Chain breaks: 1 Chain: "X" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 1} Link IDs: {'rna2p': 4, 'rna3p': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.36, per 1000 atoms: 0.25 Number of scatterers: 21690 At special positions: 0 Unit cell: (98.792, 127.684, 174.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 86 16.00 P 24 15.00 Mg 6 11.99 O 3964 8.00 N 3964 7.00 C 13640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 262 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 260 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 461 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 260 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 262 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 461 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 461 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 260 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 262 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 262 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 461 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 260 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 260 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 262 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 461 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 260 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 262 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 461 " 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5150 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 8 sheets defined 54.0% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 54 Processing helix chain 'A' and resid 72 through 91 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 105 through 120 Processing helix chain 'A' and resid 143 through 153 removed outlier: 4.087A pdb=" N GLN A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.503A pdb=" N LEU A 172 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 173 " --> pdb=" O LEU A 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 173' Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 224 through 230 removed outlier: 4.162A pdb=" N ALA A 228 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 removed outlier: 3.566A pdb=" N HIS A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.591A pdb=" N GLU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 320 through 323 removed outlier: 3.563A pdb=" N LYS A 323 " --> pdb=" O ALA A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.524A pdb=" N ASP A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.585A pdb=" N THR A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.759A pdb=" N ALA A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 435 removed outlier: 3.794A pdb=" N GLU A 435 " --> pdb=" O ALA A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 435' Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.706A pdb=" N GLY A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 477 Processing helix chain 'A' and resid 488 through 491 removed outlier: 3.509A pdb=" N ARG A 491 " --> pdb=" O HIS A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 556 through 568 removed outlier: 4.014A pdb=" N ALA A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.767A pdb=" N GLN B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 54 removed outlier: 3.759A pdb=" N GLU B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 91 Processing helix chain 'B' and resid 105 through 120 Processing helix chain 'B' and resid 143 through 153 Processing helix chain 'B' and resid 167 through 172 removed outlier: 3.745A pdb=" N LEU B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.893A pdb=" N ALA B 229 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP B 230 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 removed outlier: 3.658A pdb=" N HIS B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.590A pdb=" N HIS B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 305 through 313 removed outlier: 4.326A pdb=" N ARG B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 323 removed outlier: 3.764A pdb=" N LYS B 323 " --> pdb=" O ALA B 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 323' Processing helix chain 'B' and resid 324 through 342 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.543A pdb=" N ALA B 357 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 381 Processing helix chain 'B' and resid 404 through 420 Processing helix chain 'B' and resid 448 through 455 Processing helix chain 'B' and resid 468 through 477 Processing helix chain 'B' and resid 492 through 503 Processing helix chain 'B' and resid 509 through 517 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.578A pdb=" N THR B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 587 Processing helix chain 'B' and resid 590 through 603 removed outlier: 3.987A pdb=" N GLN B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 247 through 254 Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.869A pdb=" N HIS C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 306 through 313 Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 324 through 342 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 362 through 381 Processing helix chain 'C' and resid 404 through 420 Processing helix chain 'C' and resid 433 through 437 removed outlier: 4.092A pdb=" N ARG C 437 " --> pdb=" O PHE C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 446 Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 469 through 477 Processing helix chain 'C' and resid 492 through 503 Processing helix chain 'C' and resid 509 through 517 Processing helix chain 'C' and resid 532 through 540 Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.919A pdb=" N ALA C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 587 Processing helix chain 'C' and resid 590 through 602 Processing helix chain 'D' and resid 224 through 230 removed outlier: 3.724A pdb=" N ALA D 229 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP D 230 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 247 through 254 Processing helix chain 'D' and resid 270 through 279 removed outlier: 3.769A pdb=" N GLU D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 305 through 314 removed outlier: 4.267A pdb=" N ARG D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY D 314 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 323 removed outlier: 3.911A pdb=" N LYS D 323 " --> pdb=" O ALA D 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 324 through 342 Processing helix chain 'D' and resid 352 through 357 removed outlier: 3.560A pdb=" N ALA D 357 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 381 removed outlier: 3.525A pdb=" N THR D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 420 removed outlier: 4.003A pdb=" N ALA D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 435 removed outlier: 3.612A pdb=" N GLU D 435 " --> pdb=" O ALA D 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 432 through 435' Processing helix chain 'D' and resid 437 through 445 removed outlier: 4.048A pdb=" N ALA D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA D 442 " --> pdb=" O THR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.503A pdb=" N GLY D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 477 removed outlier: 3.834A pdb=" N ILE D 471 " --> pdb=" O ASP D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 503 Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 532 through 540 Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.980A pdb=" N ALA D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 587 Processing helix chain 'D' and resid 590 through 603 removed outlier: 3.859A pdb=" N GLN D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 230 Processing helix chain 'E' and resid 231 through 239 removed outlier: 3.540A pdb=" N HIS E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 253 removed outlier: 3.677A pdb=" N VAL E 251 " --> pdb=" O ASP E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 278 Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 305 through 313 removed outlier: 4.165A pdb=" N ARG E 309 " --> pdb=" O ILE E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 342 Processing helix chain 'E' and resid 352 through 357 removed outlier: 4.057A pdb=" N TYR E 356 " --> pdb=" O SER E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 380 Processing helix chain 'E' and resid 402 through 420 Processing helix chain 'E' and resid 432 through 436 removed outlier: 4.387A pdb=" N GLU E 435 " --> pdb=" O ALA E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 446 removed outlier: 3.760A pdb=" N ALA E 442 " --> pdb=" O THR E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 455 Processing helix chain 'E' and resid 467 through 477 Processing helix chain 'E' and resid 492 through 503 Processing helix chain 'E' and resid 509 through 517 Processing helix chain 'E' and resid 532 through 539 Processing helix chain 'E' and resid 556 through 568 removed outlier: 4.013A pdb=" N ALA E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG E 566 " --> pdb=" O LEU E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 587 Processing helix chain 'E' and resid 590 through 602 Processing helix chain 'F' and resid 224 through 230 Processing helix chain 'F' and resid 231 through 239 removed outlier: 3.687A pdb=" N HIS F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 254 Processing helix chain 'F' and resid 270 through 279 removed outlier: 3.552A pdb=" N GLU F 279 " --> pdb=" O LYS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 286 removed outlier: 3.892A pdb=" N LEU F 286 " --> pdb=" O PRO F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 313 Processing helix chain 'F' and resid 320 through 323 removed outlier: 3.802A pdb=" N LYS F 323 " --> pdb=" O ALA F 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 320 through 323' Processing helix chain 'F' and resid 324 through 342 Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 362 through 381 Processing helix chain 'F' and resid 405 through 420 Processing helix chain 'F' and resid 438 through 446 removed outlier: 3.701A pdb=" N ALA F 442 " --> pdb=" O THR F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 455 removed outlier: 3.724A pdb=" N GLY F 455 " --> pdb=" O VAL F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 477 Processing helix chain 'F' and resid 488 through 491 removed outlier: 3.821A pdb=" N ARG F 491 " --> pdb=" O HIS F 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 488 through 491' Processing helix chain 'F' and resid 492 through 503 Processing helix chain 'F' and resid 509 through 517 Processing helix chain 'F' and resid 532 through 539 Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.864A pdb=" N ALA F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG F 566 " --> pdb=" O LEU F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 587 Processing helix chain 'F' and resid 590 through 602 Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 164 removed outlier: 6.134A pdb=" N VAL A 124 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N CYS A 122 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG A 97 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE A 125 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 99 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 127 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 3 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N CYS A 100 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 5 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N HIS A 189 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 61 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL A 191 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG A 63 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 262 removed outlier: 4.440A pdb=" N VAL A 257 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 348 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU A 259 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ARG A 350 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS A 261 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 345 " --> pdb=" O HIS A 388 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASN A 390 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA A 347 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU A 392 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE A 349 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR A 394 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS A 351 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 11.667A pdb=" N VAL A 389 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N GLY A 428 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 391 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASP A 430 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A 393 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A 458 " --> pdb=" O ARG A 482 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLY A 484 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL A 460 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 483 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 506 " --> pdb=" O THR A 544 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.906A pdb=" N ARG B 97 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE B 125 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE B 99 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL B 127 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER B 7 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 4 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU B 33 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N CYS B 6 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B 30 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER B 62 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL B 32 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL B 64 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR B 34 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N HIS B 189 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE B 61 " --> pdb=" O HIS B 189 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL B 191 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG B 63 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 256 through 262 removed outlier: 7.552A pdb=" N LYS B 256 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA B 347 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU B 258 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE B 349 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N HIS B 260 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 10.097A pdb=" N CYS B 351 " --> pdb=" O HIS B 260 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N HIS B 262 " --> pdb=" O CYS B 351 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA B 345 " --> pdb=" O HIS B 388 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASN B 390 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA B 347 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU B 392 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE B 349 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 394 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N CYS B 351 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL B 427 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU B 391 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 429 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU B 393 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU B 431 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 458 " --> pdb=" O ARG B 482 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLY B 484 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL B 460 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 483 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 256 through 262 removed outlier: 7.433A pdb=" N LYS C 256 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALA C 347 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU C 258 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE C 349 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N HIS C 260 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N CYS C 351 " --> pdb=" O HIS C 260 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N HIS C 262 " --> pdb=" O CYS C 351 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS C 388 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL C 427 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU C 391 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL C 429 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU C 393 " --> pdb=" O VAL C 429 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU C 431 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 458 " --> pdb=" O ARG C 482 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLY C 484 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL C 460 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU C 483 " --> pdb=" O GLU C 507 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL C 506 " --> pdb=" O THR C 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 256 through 262 removed outlier: 6.166A pdb=" N LYS D 256 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR D 346 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS D 260 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ARG D 350 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS D 262 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA D 345 " --> pdb=" O HIS D 388 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASN D 390 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA D 347 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU D 392 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE D 349 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR D 394 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS D 351 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 11.401A pdb=" N VAL D 389 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N GLY D 428 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU D 391 " --> pdb=" O GLY D 428 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ASP D 430 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU D 393 " --> pdb=" O ASP D 430 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA D 457 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 458 " --> pdb=" O ARG D 482 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLY D 484 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL D 460 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL D 506 " --> pdb=" O THR D 544 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 256 through 262 removed outlier: 5.966A pdb=" N LYS E 256 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR E 346 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N HIS E 260 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG E 350 " --> pdb=" O HIS E 260 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N HIS E 262 " --> pdb=" O ARG E 350 " (cutoff:3.500A) removed outlier: 11.833A pdb=" N VAL E 389 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N GLY E 428 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU E 391 " --> pdb=" O GLY E 428 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASP E 430 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU E 393 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL E 458 " --> pdb=" O ARG E 482 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLY E 484 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL E 460 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU E 483 " --> pdb=" O GLU E 507 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 256 through 262 removed outlier: 6.060A pdb=" N LYS F 256 " --> pdb=" O VAL F 344 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR F 346 " --> pdb=" O LYS F 256 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS F 260 " --> pdb=" O GLU F 348 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG F 350 " --> pdb=" O HIS F 260 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N HIS F 262 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 11.651A pdb=" N VAL F 389 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLY F 428 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU F 391 " --> pdb=" O GLY F 428 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASP F 430 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU F 393 " --> pdb=" O ASP F 430 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL F 458 " --> pdb=" O ARG F 482 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY F 484 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL F 460 " --> pdb=" O GLY F 484 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU F 483 " --> pdb=" O GLU F 507 " (cutoff:3.500A) 971 hydrogen bonds defined for protein. 2751 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7395 1.34 - 1.46: 3467 1.46 - 1.57: 11216 1.57 - 1.69: 41 1.69 - 1.81: 116 Bond restraints: 22235 Sorted by residual: bond pdb=" CA PRO D 295 " pdb=" C PRO D 295 " ideal model delta sigma weight residual 1.517 1.492 0.025 6.70e-03 2.23e+04 1.42e+01 bond pdb=" CA PRO E 287 " pdb=" C PRO E 287 " ideal model delta sigma weight residual 1.514 1.498 0.017 5.50e-03 3.31e+04 9.21e+00 bond pdb=" N ASP A 315 " pdb=" CA ASP A 315 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.18e-02 7.18e+03 8.07e+00 bond pdb=" N PHE C 266 " pdb=" CA PHE C 266 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.22e-02 6.72e+03 6.21e+00 bond pdb=" N ASN A 316 " pdb=" CA ASN A 316 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.33e-02 5.65e+03 5.99e+00 ... (remaining 22230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 30026 2.29 - 4.59: 332 4.59 - 6.88: 25 6.88 - 9.17: 3 9.17 - 11.47: 2 Bond angle restraints: 30388 Sorted by residual: angle pdb=" PB ATP F 701 " pdb=" O3B ATP F 701 " pdb=" PG ATP F 701 " ideal model delta sigma weight residual 139.87 130.63 9.24 1.00e+00 1.00e+00 8.54e+01 angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 130.78 9.09 1.00e+00 1.00e+00 8.26e+01 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 132.37 7.50 1.00e+00 1.00e+00 5.63e+01 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 132.62 7.25 1.00e+00 1.00e+00 5.25e+01 angle pdb=" PB ATP C 701 " pdb=" O3B ATP C 701 " pdb=" PG ATP C 701 " ideal model delta sigma weight residual 139.87 133.73 6.14 1.00e+00 1.00e+00 3.77e+01 ... (remaining 30383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.69: 12635 20.69 - 41.39: 625 41.39 - 62.08: 180 62.08 - 82.77: 20 82.77 - 103.47: 7 Dihedral angle restraints: 13467 sinusoidal: 5538 harmonic: 7929 Sorted by residual: dihedral pdb=" CA ILE A 224 " pdb=" C ILE A 224 " pdb=" N PRO A 225 " pdb=" CA PRO A 225 " ideal model delta harmonic sigma weight residual -180.00 -157.87 -22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASP C 342 " pdb=" CB ASP C 342 " pdb=" CG ASP C 342 " pdb=" OD1 ASP C 342 " ideal model delta sinusoidal sigma weight residual -30.00 -89.03 59.03 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP A 324 " pdb=" CB ASP A 324 " pdb=" CG ASP A 324 " pdb=" OD1 ASP A 324 " ideal model delta sinusoidal sigma weight residual -30.00 -88.18 58.18 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 13464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2741 0.050 - 0.101: 527 0.101 - 0.151: 116 0.151 - 0.201: 0 0.201 - 0.251: 1 Chirality restraints: 3385 Sorted by residual: chirality pdb=" CG LEU A 222 " pdb=" CB LEU A 222 " pdb=" CD1 LEU A 222 " pdb=" CD2 LEU A 222 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA PRO A 225 " pdb=" N PRO A 225 " pdb=" C PRO A 225 " pdb=" CB PRO A 225 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 224 " pdb=" N ILE B 224 " pdb=" C ILE B 224 " pdb=" CB ILE B 224 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 3382 not shown) Planarity restraints: 3945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 56 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO B 57 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 175 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO A 176 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 186 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO A 187 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " 0.022 5.00e-02 4.00e+02 ... (remaining 3942 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 164 2.59 - 3.16: 18237 3.16 - 3.74: 34770 3.74 - 4.32: 47215 4.32 - 4.90: 79671 Nonbonded interactions: 180057 Sorted by model distance: nonbonded pdb=" OD1 ASP D 548 " pdb="ZN ZN D 702 " model vdw 2.007 2.230 nonbonded pdb=" OD1 ASP A 548 " pdb="ZN ZN A 702 " model vdw 2.015 2.230 nonbonded pdb=" OD1 ASP C 548 " pdb="ZN ZN C 702 " model vdw 2.018 2.230 nonbonded pdb=" OD1 ASP B 548 " pdb="ZN ZN B 702 " model vdw 2.021 2.230 nonbonded pdb=" OD1 ASP F 548 " pdb="ZN ZN F 702 " model vdw 2.022 2.230 ... (remaining 180052 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 'A' and (resid 1 through 396 or (resid 397 and (name N or name CA or name \ C or name O or name CB )) or resid 398 through 608 or resid 701 through 703)) selection = (chain 'B' and (resid 1 through 398 or resid 402 through 703)) } ncs_group { reference = (chain 'C' and (resid 231 through 396 or resid 404 through 703)) selection = (chain 'D' and (resid 231 through 396 or resid 404 through 703)) selection = (chain 'E' and (resid 231 through 396 or resid 404 through 703)) selection = (chain 'F' and (resid 231 through 396 or resid 404 through 703)) } 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.130 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.285 22253 Z= 0.228 Angle : 0.569 11.467 30388 Z= 0.321 Chirality : 0.042 0.251 3385 Planarity : 0.005 0.051 3945 Dihedral : 13.599 103.468 8317 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.96 % Rotamer: Outliers : 5.85 % Allowed : 7.96 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2721 helix: 1.04 (0.14), residues: 1297 sheet: 0.02 (0.33), residues: 270 loop : -0.10 (0.19), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 573 TYR 0.010 0.002 TYR F 531 PHE 0.011 0.001 PHE B 178 TRP 0.014 0.002 TRP F 364 HIS 0.004 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (22235) covalent geometry : angle 0.56867 / 0.32 (30388) hydrogen bonds : bond 0.15541 / 10.28 ( 971) hydrogen bonds : angle 5.61610 / 4.08 ( 2751) metal coordination : bond 0.06749 / 2.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 736 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 11 SER cc_start: 0.8325 (m) cc_final: 0.8008 (p) REVERT: A 14 VAL cc_start: 0.8539 (m) cc_final: 0.8284 (t) REVERT: A 34 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7667 (t) REVERT: A 118 LEU cc_start: 0.8315 (mt) cc_final: 0.8082 (mt) REVERT: A 164 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7397 (mm-30) REVERT: A 172 LEU cc_start: 0.7918 (mt) cc_final: 0.7699 (mt) REVERT: A 181 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6248 (mt-10) REVERT: A 196 MET cc_start: 0.6803 (mtm) cc_final: 0.6228 (mtm) REVERT: A 222 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7422 (pt) REVERT: A 240 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 273 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8330 (tp) REVERT: A 278 GLN cc_start: 0.8140 (mt0) cc_final: 0.7909 (mt0) REVERT: A 319 SER cc_start: 0.8644 (p) cc_final: 0.8434 (t) REVERT: A 348 GLU cc_start: 0.8726 (mt-10) cc_final: 0.7501 (tt0) REVERT: A 369 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7904 (tt0) REVERT: A 465 ASN cc_start: 0.8224 (m110) cc_final: 0.8022 (m-40) REVERT: A 507 GLU cc_start: 0.9046 (mt-10) cc_final: 0.7498 (pt0) REVERT: A 521 LEU cc_start: 0.8870 (mt) cc_final: 0.8462 (mp) REVERT: A 580 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8292 (mm110) REVERT: B 29 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6480 (mt-10) REVERT: B 131 PRO cc_start: 0.8041 (Cg_endo) cc_final: 0.7752 (Cg_exo) REVERT: B 164 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7258 (mm-30) REVERT: B 303 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8185 (mm-30) REVERT: B 376 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7905 (tm-30) REVERT: B 425 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.6663 (ptm160) REVERT: B 447 ASP cc_start: 0.8581 (t0) cc_final: 0.8327 (t0) REVERT: B 449 GLU cc_start: 0.7978 (tt0) cc_final: 0.7620 (tt0) REVERT: B 456 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8393 (mp) REVERT: B 461 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.8166 (t70) REVERT: B 507 GLU cc_start: 0.8786 (mt-10) cc_final: 0.7534 (mt-10) REVERT: B 543 VAL cc_start: 0.9099 (p) cc_final: 0.8793 (t) REVERT: B 552 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8313 (mp) REVERT: C 243 ASP cc_start: 0.8446 (t70) cc_final: 0.8209 (t70) REVERT: C 258 GLU cc_start: 0.8068 (tp30) cc_final: 0.7791 (tp30) REVERT: C 279 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7893 (mm-30) REVERT: C 342 ASP cc_start: 0.7969 (t70) cc_final: 0.7659 (t0) REVERT: C 408 ARG cc_start: 0.8508 (mtt180) cc_final: 0.8287 (mtt180) REVERT: C 418 GLU cc_start: 0.7778 (tp30) cc_final: 0.7551 (tp30) REVERT: C 430 ASP cc_start: 0.8254 (t70) cc_final: 0.8012 (t0) REVERT: C 461 HIS cc_start: 0.9121 (OUTLIER) cc_final: 0.8676 (m90) REVERT: C 469 GLU cc_start: 0.7558 (tp30) cc_final: 0.7305 (tp30) REVERT: C 517 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8575 (mmmt) REVERT: C 556 SER cc_start: 0.8516 (t) cc_final: 0.8157 (t) REVERT: C 557 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7724 (tp) REVERT: C 591 GLN cc_start: 0.8137 (tp40) cc_final: 0.7900 (tp40) REVERT: D 240 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7581 (mt-10) REVERT: D 245 VAL cc_start: 0.8921 (m) cc_final: 0.8614 (p) REVERT: D 248 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8116 (tmmm) REVERT: D 278 GLN cc_start: 0.7327 (mt0) cc_final: 0.7053 (mt0) REVERT: D 386 ARG cc_start: 0.8772 (ttm170) cc_final: 0.8555 (ttm170) REVERT: D 440 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7264 (ttm170) REVERT: D 465 ASN cc_start: 0.5026 (OUTLIER) cc_final: 0.4520 (t0) REVERT: E 279 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: E 329 ARG cc_start: 0.8307 (ttp-110) cc_final: 0.7950 (ttp-110) REVERT: E 337 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: E 342 ASP cc_start: 0.8696 (t70) cc_final: 0.8403 (t0) REVERT: E 429 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8822 (m) REVERT: E 464 GLU cc_start: 0.8057 (tt0) cc_final: 0.7820 (tt0) REVERT: E 465 ASN cc_start: 0.8332 (m110) cc_final: 0.7995 (m-40) REVERT: E 467 ASP cc_start: 0.7674 (m-30) cc_final: 0.7414 (m-30) REVERT: E 495 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8624 (tt) REVERT: F 243 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: F 380 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: F 436 ASP cc_start: 0.7664 (t70) cc_final: 0.7395 (t70) REVERT: F 465 ASN cc_start: 0.6703 (OUTLIER) cc_final: 0.6485 (m-40) REVERT: F 491 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7351 (tpm170) REVERT: F 496 LEU cc_start: 0.8842 (tm) cc_final: 0.8576 (tp) REVERT: F 575 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7855 (mp0) outliers start: 130 outliers final: 32 residues processed: 805 average time/residue: 0.7735 time to fit residues: 690.7659 Evaluate side-chains 662 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 609 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 425 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 434 PHE Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 479 SER Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 525 GLN Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 422 ASN Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 491 ARG Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 525 GLN Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 575 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 89 GLN A 93 GLN A 169 GLN A 211 HIS A 278 GLN A 355 ASN A 513 ASN A 515 GLN B 20 GLN B 65 GLN B 76 HIS B 89 GLN B 136 GLN B 185 GLN B 239 HIS B 465 ASN B 485 HIS B 513 ASN C 246 GLN C 252 GLN C 269 HIS C 316 ASN C 422 ASN C 515 GLN C 546 ASN C 560 ASN ** D 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN D 316 ASN D 355 ASN D 390 ASN D 409 HIS D 515 GLN D 525 GLN D 549 ASN D 603 GLN E 239 HIS E 246 GLN E 316 ASN E 317 ASN E 375 GLN E 376 GLN E 390 ASN E 465 ASN E 513 ASN E 525 GLN ** E 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 GLN E 591 GLN F 239 HIS F 252 GLN F 278 GLN F 355 ASN F 372 ASN F 376 GLN F 390 ASN F 409 HIS F 419 HIS F 465 ASN F 515 GLN F 525 GLN F 546 ASN ** F 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 GLN F 591 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.100671 restraints weight = 33963.044| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.06 r_work: 0.3216 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22253 Z= 0.161 Angle : 0.583 12.816 30388 Z= 0.289 Chirality : 0.042 0.238 3385 Planarity : 0.005 0.055 3945 Dihedral : 10.544 106.636 3381 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 5.26 % Allowed : 16.19 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.16), residues: 2721 helix: 1.32 (0.14), residues: 1327 sheet: 0.02 (0.33), residues: 270 loop : -0.03 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 333 TYR 0.011 0.001 TYR C 356 PHE 0.021 0.001 PHE B 125 TRP 0.013 0.002 TRP F 364 HIS 0.008 0.001 HIS F 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (22235) covalent geometry : angle 0.58293 / 0.29 (30388) hydrogen bonds : bond 0.04329 / 2.84 ( 971) hydrogen bonds : angle 4.67583 / 3.38 ( 2751) metal coordination : bond 0.00388 / 0.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 614 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 11 SER cc_start: 0.8832 (m) cc_final: 0.8552 (p) REVERT: A 14 VAL cc_start: 0.8574 (m) cc_final: 0.8372 (t) REVERT: A 63 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6473 (ptm160) REVERT: A 93 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7695 (mm110) REVERT: A 123 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7113 (tm-30) REVERT: A 147 VAL cc_start: 0.8473 (t) cc_final: 0.8165 (p) REVERT: A 199 ARG cc_start: 0.8253 (ttt-90) cc_final: 0.8032 (ttt-90) REVERT: A 219 ILE cc_start: 0.6756 (tt) cc_final: 0.6492 (tt) REVERT: A 222 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7557 (pt) REVERT: A 246 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7819 (mm-40) REVERT: A 273 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8063 (tp) REVERT: A 337 GLU cc_start: 0.8223 (tp30) cc_final: 0.7996 (tp30) REVERT: A 348 GLU cc_start: 0.8790 (mt-10) cc_final: 0.7923 (mt-10) REVERT: A 369 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8181 (mt-10) REVERT: A 379 GLU cc_start: 0.8436 (tt0) cc_final: 0.8109 (mt-10) REVERT: A 465 ASN cc_start: 0.8214 (m110) cc_final: 0.7895 (m-40) REVERT: A 507 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8275 (pt0) REVERT: A 523 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7254 (mm-30) REVERT: A 580 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8298 (mm110) REVERT: B 164 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 167 TRP cc_start: 0.8327 (m-10) cc_final: 0.7906 (m-10) REVERT: B 195 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7123 (p0) REVERT: B 279 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 303 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8217 (mm-30) REVERT: B 315 ASP cc_start: 0.8365 (m-30) cc_final: 0.8105 (m-30) REVERT: B 369 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 376 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 449 GLU cc_start: 0.7830 (tt0) cc_final: 0.7527 (tt0) REVERT: B 456 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8446 (pt) REVERT: B 461 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.8176 (t70) REVERT: B 507 GLU cc_start: 0.8869 (mt-10) cc_final: 0.7535 (mt-10) REVERT: B 543 VAL cc_start: 0.8991 (p) cc_final: 0.8628 (t) REVERT: B 552 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8079 (mp) REVERT: B 557 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8276 (tt) REVERT: C 243 ASP cc_start: 0.8373 (t70) cc_final: 0.8094 (t0) REVERT: C 258 GLU cc_start: 0.8032 (tp30) cc_final: 0.7734 (tp30) REVERT: C 279 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7938 (mm-30) REVERT: C 315 ASP cc_start: 0.8472 (m-30) cc_final: 0.7997 (m-30) REVERT: C 342 ASP cc_start: 0.8040 (t70) cc_final: 0.7749 (t70) REVERT: C 418 GLU cc_start: 0.8043 (tp30) cc_final: 0.7777 (tp30) REVERT: C 421 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8481 (mmmm) REVERT: C 430 ASP cc_start: 0.8401 (t70) cc_final: 0.8086 (t0) REVERT: C 461 HIS cc_start: 0.9128 (OUTLIER) cc_final: 0.8513 (m90) REVERT: C 467 ASP cc_start: 0.6223 (OUTLIER) cc_final: 0.5884 (p0) REVERT: C 515 GLN cc_start: 0.8673 (mt0) cc_final: 0.8472 (mt0) REVERT: C 553 SER cc_start: 0.8945 (m) cc_final: 0.8703 (m) REVERT: C 556 SER cc_start: 0.8448 (t) cc_final: 0.8170 (t) REVERT: C 566 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.8038 (mtp-110) REVERT: C 591 GLN cc_start: 0.8192 (tp40) cc_final: 0.7864 (tp40) REVERT: D 245 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8607 (p) REVERT: D 278 GLN cc_start: 0.7440 (mt0) cc_final: 0.7076 (mt0) REVERT: D 302 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7437 (mm-30) REVERT: D 311 MET cc_start: 0.8298 (mtm) cc_final: 0.7993 (mtm) REVERT: D 418 GLU cc_start: 0.8106 (tt0) cc_final: 0.7882 (tm-30) REVERT: D 453 ARG cc_start: 0.8287 (tpp80) cc_final: 0.8049 (mmm160) REVERT: D 513 ASN cc_start: 0.8898 (m-40) cc_final: 0.8539 (m-40) REVERT: D 523 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: D 525 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8074 (pp30) REVERT: D 531 TYR cc_start: 0.8731 (t80) cc_final: 0.8508 (t80) REVERT: E 222 LEU cc_start: 0.8288 (mt) cc_final: 0.8053 (mt) REVERT: E 236 ARG cc_start: 0.8346 (mmt180) cc_final: 0.8101 (mtt180) REVERT: E 279 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: E 329 ARG cc_start: 0.8116 (ttp-110) cc_final: 0.7700 (ttp-110) REVERT: E 333 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7937 (mtp180) REVERT: E 342 ASP cc_start: 0.8680 (t70) cc_final: 0.8374 (t0) REVERT: E 464 GLU cc_start: 0.8280 (tt0) cc_final: 0.7988 (tt0) REVERT: E 548 ASP cc_start: 0.7803 (t70) cc_final: 0.7572 (t0) REVERT: E 554 GLN cc_start: 0.8918 (tt0) cc_final: 0.8663 (tt0) REVERT: F 243 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7891 (m-30) REVERT: F 302 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7713 (mm-30) REVERT: F 380 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: F 436 ASP cc_start: 0.7894 (t70) cc_final: 0.7462 (t0) REVERT: F 437 ARG cc_start: 0.7784 (mtm180) cc_final: 0.7522 (mtm-85) REVERT: F 465 ASN cc_start: 0.6324 (OUTLIER) cc_final: 0.5836 (m-40) REVERT: F 473 GLN cc_start: 0.8799 (mm110) cc_final: 0.8391 (mt0) REVERT: F 523 GLU cc_start: 0.8013 (tp30) cc_final: 0.7318 (tp30) REVERT: F 525 GLN cc_start: 0.8225 (pm20) cc_final: 0.7647 (pm20) REVERT: F 574 LEU cc_start: 0.8414 (tm) cc_final: 0.8213 (tp) REVERT: F 575 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: F 585 GLN cc_start: 0.8752 (mt0) cc_final: 0.8468 (mt0) outliers start: 117 outliers final: 49 residues processed: 680 average time/residue: 0.8252 time to fit residues: 619.7914 Evaluate side-chains 651 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 580 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 434 PHE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 525 GLN Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain E residue 256 LYS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 524 GLU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 243 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 380 GLU Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 491 ARG Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 575 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 114 optimal weight: 0.0770 chunk 115 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 409 HIS A 525 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN B 282 ASN B 465 ASN B 580 GLN C 375 GLN C 485 HIS C 546 ASN C 560 ASN D 409 HIS D 485 HIS D 515 GLN D 546 ASN D 554 GLN E 546 ASN E 549 ASN E 560 ASN F 282 ASN F 409 HIS ** F 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.100368 restraints weight = 34194.509| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.09 r_work: 0.3208 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22253 Z= 0.152 Angle : 0.552 12.219 30388 Z= 0.272 Chirality : 0.042 0.238 3385 Planarity : 0.005 0.053 3945 Dihedral : 9.820 106.761 3342 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.98 % Favored : 96.91 % Rotamer: Outliers : 6.12 % Allowed : 17.85 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 2721 helix: 1.39 (0.14), residues: 1331 sheet: -0.05 (0.32), residues: 270 loop : 0.00 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 290 TYR 0.009 0.001 TYR E 531 PHE 0.014 0.001 PHE B 125 TRP 0.020 0.001 TRP C 237 HIS 0.006 0.001 HIS F 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (22235) covalent geometry : angle 0.55184 / 0.27 (30388) hydrogen bonds : bond 0.03901 / 2.57 ( 971) hydrogen bonds : angle 4.49005 / 3.25 ( 2751) metal coordination : bond 0.00234 / 0.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 604 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8778 (m) cc_final: 0.8519 (p) REVERT: A 147 VAL cc_start: 0.8498 (t) cc_final: 0.8285 (p) REVERT: A 164 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8221 (mm-30) REVERT: A 222 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7638 (pt) REVERT: A 273 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8047 (tp) REVERT: A 324 ASP cc_start: 0.8280 (t0) cc_final: 0.8054 (t0) REVERT: A 337 GLU cc_start: 0.8342 (tp30) cc_final: 0.8088 (tp30) REVERT: A 348 GLU cc_start: 0.8860 (mt-10) cc_final: 0.7974 (mt-10) REVERT: A 379 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: A 465 ASN cc_start: 0.8332 (m110) cc_final: 0.7955 (m-40) REVERT: A 496 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8362 (tp) REVERT: A 501 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: A 507 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8229 (pt0) REVERT: A 523 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7335 (mm-30) REVERT: A 525 GLN cc_start: 0.8181 (mt0) cc_final: 0.7966 (mt0) REVERT: A 534 ARG cc_start: 0.8922 (mmm-85) cc_final: 0.8486 (mtp85) REVERT: A 580 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8300 (mm110) REVERT: B 48 LEU cc_start: 0.8460 (mt) cc_final: 0.8253 (mt) REVERT: B 160 ARG cc_start: 0.8398 (ptp-110) cc_final: 0.8043 (mtm-85) REVERT: B 164 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 167 TRP cc_start: 0.8319 (m-10) cc_final: 0.7899 (m-10) REVERT: B 195 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7225 (p0) REVERT: B 203 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: B 279 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 315 ASP cc_start: 0.8447 (m-30) cc_final: 0.8214 (m-30) REVERT: B 369 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7809 (mt-10) REVERT: B 376 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7545 (tm-30) REVERT: B 449 GLU cc_start: 0.7879 (tt0) cc_final: 0.7662 (tt0) REVERT: B 461 HIS cc_start: 0.8574 (OUTLIER) cc_final: 0.8230 (t70) REVERT: B 507 GLU cc_start: 0.8888 (mt-10) cc_final: 0.7273 (pt0) REVERT: B 557 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8205 (tt) REVERT: C 243 ASP cc_start: 0.8383 (t70) cc_final: 0.8118 (t0) REVERT: C 258 GLU cc_start: 0.8083 (tp30) cc_final: 0.7681 (tp30) REVERT: C 279 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 315 ASP cc_start: 0.8503 (m-30) cc_final: 0.8072 (m-30) REVERT: C 324 ASP cc_start: 0.8134 (m-30) cc_final: 0.7915 (m-30) REVERT: C 333 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.7989 (mmm-85) REVERT: C 342 ASP cc_start: 0.8118 (t70) cc_final: 0.7804 (t70) REVERT: C 418 GLU cc_start: 0.8068 (tp30) cc_final: 0.7822 (tp30) REVERT: C 421 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8374 (mmmm) REVERT: C 430 ASP cc_start: 0.8472 (t70) cc_final: 0.8196 (t0) REVERT: C 461 HIS cc_start: 0.9200 (OUTLIER) cc_final: 0.8523 (m90) REVERT: C 467 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5867 (p0) REVERT: C 495 LEU cc_start: 0.8010 (tm) cc_final: 0.7750 (tp) REVERT: C 522 ASP cc_start: 0.6839 (t0) cc_final: 0.6568 (t0) REVERT: C 556 SER cc_start: 0.8434 (t) cc_final: 0.8204 (t) REVERT: C 568 CYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7737 (p) REVERT: C 591 GLN cc_start: 0.8231 (tp40) cc_final: 0.7912 (tp40) REVERT: D 245 VAL cc_start: 0.8853 (m) cc_final: 0.8641 (p) REVERT: D 248 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7991 (tmmm) REVERT: D 278 GLN cc_start: 0.7376 (mt0) cc_final: 0.7085 (mt0) REVERT: D 309 ARG cc_start: 0.8345 (mtm180) cc_final: 0.8143 (mtm180) REVERT: D 311 MET cc_start: 0.8261 (mtm) cc_final: 0.7964 (mtm) REVERT: D 378 MET cc_start: 0.8768 (mtm) cc_final: 0.8556 (mtp) REVERT: D 418 GLU cc_start: 0.8070 (tt0) cc_final: 0.7864 (tm-30) REVERT: D 430 ASP cc_start: 0.8578 (t0) cc_final: 0.8371 (t0) REVERT: D 453 ARG cc_start: 0.8296 (tpp80) cc_final: 0.8035 (mmm-85) REVERT: D 464 GLU cc_start: 0.5663 (OUTLIER) cc_final: 0.5395 (tt0) REVERT: D 513 ASN cc_start: 0.8971 (m-40) cc_final: 0.8582 (m-40) REVERT: D 525 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8040 (pp30) REVERT: D 531 TYR cc_start: 0.8754 (t80) cc_final: 0.8521 (t80) REVERT: E 222 LEU cc_start: 0.8331 (mt) cc_final: 0.8117 (mt) REVERT: E 236 ARG cc_start: 0.8327 (mmt180) cc_final: 0.8085 (mtt180) REVERT: E 275 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8288 (mtmm) REVERT: E 279 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: E 329 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7743 (ttp-110) REVERT: E 342 ASP cc_start: 0.8689 (t70) cc_final: 0.8378 (t0) REVERT: E 449 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: E 525 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7454 (tm-30) REVERT: E 537 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8542 (mt) REVERT: F 302 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7630 (mm-30) REVERT: F 436 ASP cc_start: 0.7960 (t70) cc_final: 0.7464 (t0) REVERT: F 473 GLN cc_start: 0.8793 (mm110) cc_final: 0.8443 (mt0) REVERT: F 496 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8374 (tp) REVERT: F 523 GLU cc_start: 0.8048 (tp30) cc_final: 0.7345 (tp30) REVERT: F 525 GLN cc_start: 0.8207 (pm20) cc_final: 0.7623 (pm20) REVERT: F 575 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: F 585 GLN cc_start: 0.8811 (mt0) cc_final: 0.8572 (mt0) outliers start: 136 outliers final: 66 residues processed: 681 average time/residue: 0.8367 time to fit residues: 630.6897 Evaluate side-chains 665 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 578 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 434 PHE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 525 GLN Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 524 GLU Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 491 ARG Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 575 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 87 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS B 54 HIS B 282 ASN B 419 HIS B 465 ASN C 546 ASN D 355 ASN D 409 HIS D 515 GLN D 546 ASN D 580 GLN E 317 ASN E 355 ASN E 546 ASN F 409 HIS F 465 ASN F 485 HIS F 560 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099829 restraints weight = 33872.011| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.06 r_work: 0.3214 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22253 Z= 0.159 Angle : 0.551 12.356 30388 Z= 0.271 Chirality : 0.042 0.249 3385 Planarity : 0.004 0.053 3945 Dihedral : 9.429 107.547 3325 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 5.76 % Allowed : 19.83 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.16), residues: 2721 helix: 1.41 (0.14), residues: 1331 sheet: -0.07 (0.31), residues: 277 loop : 0.06 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 290 TYR 0.011 0.001 TYR C 356 PHE 0.011 0.001 PHE B 125 TRP 0.025 0.001 TRP C 237 HIS 0.011 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (22235) covalent geometry : angle 0.55111 / 0.27 (30388) hydrogen bonds : bond 0.03772 / 2.48 ( 971) hydrogen bonds : angle 4.42864 / 3.20 ( 2751) metal coordination : bond 0.00256 / 0.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 592 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 11 SER cc_start: 0.8799 (m) cc_final: 0.8545 (p) REVERT: A 28 ASP cc_start: 0.8119 (m-30) cc_final: 0.7836 (m-30) REVERT: A 147 VAL cc_start: 0.8501 (t) cc_final: 0.8274 (p) REVERT: A 164 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8171 (mm-30) REVERT: A 219 ILE cc_start: 0.6836 (tt) cc_final: 0.6345 (tt) REVERT: A 222 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7686 (pt) REVERT: A 273 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8062 (tp) REVERT: A 290 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8146 (mtm-85) REVERT: A 337 GLU cc_start: 0.8346 (tp30) cc_final: 0.8082 (tp30) REVERT: A 348 GLU cc_start: 0.8871 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 369 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8074 (mt-10) REVERT: A 379 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: A 465 ASN cc_start: 0.8347 (m110) cc_final: 0.7993 (m-40) REVERT: A 496 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8374 (tp) REVERT: A 501 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: A 507 GLU cc_start: 0.9125 (mt-10) cc_final: 0.7656 (pt0) REVERT: A 523 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7354 (mm-30) REVERT: A 525 GLN cc_start: 0.8234 (mt0) cc_final: 0.8017 (mt0) REVERT: A 580 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8269 (mm110) REVERT: B 148 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7438 (tp30) REVERT: B 160 ARG cc_start: 0.8366 (ptp-110) cc_final: 0.7933 (mtm110) REVERT: B 164 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7709 (mm-30) REVERT: B 167 TRP cc_start: 0.8349 (m-10) cc_final: 0.7897 (m-10) REVERT: B 195 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7234 (p0) REVERT: B 203 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: B 245 VAL cc_start: 0.9229 (t) cc_final: 0.8983 (m) REVERT: B 279 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7952 (mt-10) REVERT: B 315 ASP cc_start: 0.8473 (m-30) cc_final: 0.8268 (m-30) REVERT: B 369 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7792 (mt-10) REVERT: B 376 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7498 (tm-30) REVERT: B 430 ASP cc_start: 0.8178 (t0) cc_final: 0.7889 (t0) REVERT: B 449 GLU cc_start: 0.7874 (tt0) cc_final: 0.7653 (tt0) REVERT: B 461 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.8258 (t70) REVERT: B 507 GLU cc_start: 0.8887 (mt-10) cc_final: 0.7269 (pt0) REVERT: B 557 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8219 (tt) REVERT: C 243 ASP cc_start: 0.8389 (t70) cc_final: 0.8105 (t0) REVERT: C 258 GLU cc_start: 0.8047 (tp30) cc_final: 0.7628 (tp30) REVERT: C 279 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8001 (mm-30) REVERT: C 315 ASP cc_start: 0.8294 (m-30) cc_final: 0.7884 (m-30) REVERT: C 324 ASP cc_start: 0.8096 (m-30) cc_final: 0.7880 (m-30) REVERT: C 333 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7994 (mmm-85) REVERT: C 342 ASP cc_start: 0.8123 (t70) cc_final: 0.7785 (t70) REVERT: C 418 GLU cc_start: 0.8091 (tp30) cc_final: 0.7863 (tp30) REVERT: C 421 LYS cc_start: 0.8749 (mmmm) cc_final: 0.8370 (mmmm) REVERT: C 430 ASP cc_start: 0.8450 (t70) cc_final: 0.8163 (t0) REVERT: C 461 HIS cc_start: 0.9202 (OUTLIER) cc_final: 0.8486 (m90) REVERT: C 467 ASP cc_start: 0.6086 (OUTLIER) cc_final: 0.5768 (p0) REVERT: C 556 SER cc_start: 0.8405 (t) cc_final: 0.8123 (t) REVERT: C 571 ILE cc_start: 0.8419 (pt) cc_final: 0.8046 (mt) REVERT: C 591 GLN cc_start: 0.8202 (tp40) cc_final: 0.7903 (tp40) REVERT: D 248 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7950 (tmmm) REVERT: D 311 MET cc_start: 0.8213 (mtm) cc_final: 0.7895 (mtm) REVERT: D 324 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8081 (t0) REVERT: D 342 ASP cc_start: 0.8664 (t0) cc_final: 0.8271 (t0) REVERT: D 378 MET cc_start: 0.8761 (mtm) cc_final: 0.8557 (mtp) REVERT: D 453 ARG cc_start: 0.8300 (tpp80) cc_final: 0.8088 (mmm160) REVERT: D 464 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.5443 (tt0) REVERT: D 465 ASN cc_start: 0.5142 (OUTLIER) cc_final: 0.4887 (t0) REVERT: D 513 ASN cc_start: 0.9010 (m-40) cc_final: 0.8602 (m-40) REVERT: D 525 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8053 (pp30) REVERT: D 531 TYR cc_start: 0.8740 (t80) cc_final: 0.8507 (t80) REVERT: E 222 LEU cc_start: 0.8329 (mt) cc_final: 0.8117 (mt) REVERT: E 236 ARG cc_start: 0.8212 (mmt180) cc_final: 0.7883 (mtt-85) REVERT: E 275 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8289 (mtmm) REVERT: E 279 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: E 329 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7705 (ttp-110) REVERT: E 333 ARG cc_start: 0.8321 (mtp85) cc_final: 0.8040 (mtp180) REVERT: E 342 ASP cc_start: 0.8699 (t70) cc_final: 0.8393 (t0) REVERT: E 449 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: E 495 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8612 (tt) REVERT: E 525 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7449 (tm-30) REVERT: E 537 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8563 (mt) REVERT: F 243 ASP cc_start: 0.8092 (m-30) cc_final: 0.7744 (m-30) REVERT: F 302 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7651 (mm-30) REVERT: F 436 ASP cc_start: 0.7954 (t70) cc_final: 0.7389 (t0) REVERT: F 465 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6262 (m-40) REVERT: F 473 GLN cc_start: 0.8790 (mt0) cc_final: 0.8461 (mt0) REVERT: F 496 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8348 (tp) REVERT: F 523 GLU cc_start: 0.8082 (tp30) cc_final: 0.7429 (tp30) REVERT: F 525 GLN cc_start: 0.8265 (pm20) cc_final: 0.7653 (pm20) REVERT: F 575 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: F 585 GLN cc_start: 0.8813 (mt0) cc_final: 0.8590 (mt0) outliers start: 128 outliers final: 74 residues processed: 667 average time/residue: 0.8209 time to fit residues: 604.9439 Evaluate side-chains 676 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 578 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 434 PHE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 525 GLN Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 606 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 465 ASN Chi-restraints excluded: chain F residue 491 ARG Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 575 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 28 optimal weight: 0.4980 chunk 90 optimal weight: 0.2980 chunk 241 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 230 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 226 optimal weight: 0.7980 chunk 188 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 211 HIS A 409 HIS A 473 GLN B 282 ASN B 422 ASN B 465 ASN C 331 GLN C 372 ASN C 409 HIS C 546 ASN D 316 ASN D 355 ASN D 409 HIS D 515 GLN E 355 ASN E 485 HIS F 409 HIS F 603 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100544 restraints weight = 33894.565| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.08 r_work: 0.3216 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22253 Z= 0.136 Angle : 0.545 12.132 30388 Z= 0.268 Chirality : 0.041 0.229 3385 Planarity : 0.004 0.059 3945 Dihedral : 9.315 107.314 3324 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 5.49 % Allowed : 21.31 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 2721 helix: 1.48 (0.14), residues: 1334 sheet: -0.11 (0.31), residues: 276 loop : 0.02 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 290 TYR 0.009 0.001 TYR B 336 PHE 0.011 0.001 PHE C 476 TRP 0.022 0.001 TRP C 237 HIS 0.007 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (22235) covalent geometry : angle 0.54459 / 0.27 (30388) hydrogen bonds : bond 0.03572 / 2.35 ( 971) hydrogen bonds : angle 4.33822 / 3.13 ( 2751) metal coordination : bond 0.00195 / 0.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 592 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8804 (m) cc_final: 0.8559 (p) REVERT: A 28 ASP cc_start: 0.8138 (m-30) cc_final: 0.7835 (m-30) REVERT: A 140 GLU cc_start: 0.8358 (mp0) cc_final: 0.7960 (mm-30) REVERT: A 147 VAL cc_start: 0.8503 (t) cc_final: 0.8262 (p) REVERT: A 164 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8165 (mm-30) REVERT: A 221 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7884 (mp0) REVERT: A 222 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7723 (pt) REVERT: A 324 ASP cc_start: 0.8262 (t0) cc_final: 0.8051 (t0) REVERT: A 337 GLU cc_start: 0.8333 (tp30) cc_final: 0.8077 (tp30) REVERT: A 379 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: A 465 ASN cc_start: 0.8398 (m110) cc_final: 0.8085 (m-40) REVERT: A 496 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8372 (tp) REVERT: A 525 GLN cc_start: 0.8214 (mt0) cc_final: 0.7744 (mt0) REVERT: A 580 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8277 (mm110) REVERT: B 30 VAL cc_start: 0.8479 (t) cc_final: 0.8169 (p) REVERT: B 65 GLN cc_start: 0.7460 (tp40) cc_final: 0.6998 (tt0) REVERT: B 160 ARG cc_start: 0.8337 (ptp-110) cc_final: 0.7891 (mtm110) REVERT: B 164 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 167 TRP cc_start: 0.8361 (m-10) cc_final: 0.7914 (m-10) REVERT: B 195 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7229 (p0) REVERT: B 245 VAL cc_start: 0.9223 (t) cc_final: 0.8981 (m) REVERT: B 279 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7890 (mt-10) REVERT: B 315 ASP cc_start: 0.8505 (m-30) cc_final: 0.8298 (m-30) REVERT: B 369 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7839 (mt-10) REVERT: B 430 ASP cc_start: 0.8176 (t0) cc_final: 0.7947 (t0) REVERT: B 437 ARG cc_start: 0.7848 (mmp80) cc_final: 0.7620 (mmp80) REVERT: B 449 GLU cc_start: 0.7918 (tt0) cc_final: 0.7685 (tt0) REVERT: B 507 GLU cc_start: 0.8893 (mt-10) cc_final: 0.7658 (pt0) REVERT: B 548 ASP cc_start: 0.7953 (t70) cc_final: 0.7543 (t0) REVERT: C 243 ASP cc_start: 0.8370 (t70) cc_final: 0.8111 (t0) REVERT: C 258 GLU cc_start: 0.8046 (tp30) cc_final: 0.7619 (tp30) REVERT: C 279 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8048 (mm-30) REVERT: C 315 ASP cc_start: 0.8131 (m-30) cc_final: 0.7755 (m-30) REVERT: C 324 ASP cc_start: 0.8072 (m-30) cc_final: 0.7847 (m-30) REVERT: C 342 ASP cc_start: 0.8119 (t70) cc_final: 0.7761 (t70) REVERT: C 379 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: C 418 GLU cc_start: 0.8064 (tp30) cc_final: 0.7842 (tp30) REVERT: C 430 ASP cc_start: 0.8456 (t70) cc_final: 0.8165 (t0) REVERT: C 461 HIS cc_start: 0.9196 (OUTLIER) cc_final: 0.8454 (m90) REVERT: C 467 ASP cc_start: 0.6043 (OUTLIER) cc_final: 0.5803 (p0) REVERT: C 497 ARG cc_start: 0.7638 (ttt180) cc_final: 0.7411 (ttt180) REVERT: C 522 ASP cc_start: 0.6709 (t0) cc_final: 0.6350 (t0) REVERT: C 556 SER cc_start: 0.8415 (t) cc_final: 0.8181 (t) REVERT: C 571 ILE cc_start: 0.8405 (pt) cc_final: 0.8039 (mt) REVERT: C 591 GLN cc_start: 0.8207 (tp40) cc_final: 0.7908 (tp40) REVERT: D 290 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7278 (mtm-85) REVERT: D 311 MET cc_start: 0.8211 (mtm) cc_final: 0.7904 (mtm) REVERT: D 324 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8077 (t0) REVERT: D 342 ASP cc_start: 0.8608 (t0) cc_final: 0.8234 (t0) REVERT: D 418 GLU cc_start: 0.8055 (tt0) cc_final: 0.7833 (tm-30) REVERT: D 453 ARG cc_start: 0.8310 (tpp80) cc_final: 0.8075 (mmm160) REVERT: D 464 GLU cc_start: 0.5744 (OUTLIER) cc_final: 0.5473 (tt0) REVERT: D 513 ASN cc_start: 0.9010 (m-40) cc_final: 0.8634 (m-40) REVERT: D 525 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8011 (pp30) REVERT: D 531 TYR cc_start: 0.8721 (t80) cc_final: 0.8504 (t80) REVERT: D 566 ARG cc_start: 0.8837 (mtp-110) cc_final: 0.8627 (mtp-110) REVERT: E 222 LEU cc_start: 0.8317 (mt) cc_final: 0.8094 (mt) REVERT: E 236 ARG cc_start: 0.8269 (mmt180) cc_final: 0.8022 (mtt180) REVERT: E 274 HIS cc_start: 0.8491 (m-70) cc_final: 0.8244 (m90) REVERT: E 275 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8196 (mtmm) REVERT: E 279 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: E 329 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7732 (ttp-110) REVERT: E 333 ARG cc_start: 0.8309 (mtp85) cc_final: 0.8043 (mtp180) REVERT: E 342 ASP cc_start: 0.8705 (t70) cc_final: 0.8396 (t0) REVERT: E 368 GLN cc_start: 0.8484 (mt0) cc_final: 0.8274 (mt0) REVERT: E 449 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: E 495 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8609 (tt) REVERT: E 525 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7456 (tm-30) REVERT: E 554 GLN cc_start: 0.8916 (tt0) cc_final: 0.8682 (tt0) REVERT: F 243 ASP cc_start: 0.8087 (m-30) cc_final: 0.7754 (m-30) REVERT: F 302 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7689 (mm-30) REVERT: F 436 ASP cc_start: 0.7843 (t70) cc_final: 0.7286 (t0) REVERT: F 437 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7806 (mtm-85) REVERT: F 473 GLN cc_start: 0.8795 (mt0) cc_final: 0.8463 (mt0) REVERT: F 496 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8322 (tp) REVERT: F 523 GLU cc_start: 0.8115 (tp30) cc_final: 0.7538 (tp30) REVERT: F 525 GLN cc_start: 0.8287 (pm20) cc_final: 0.7679 (pm20) REVERT: F 575 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: F 585 GLN cc_start: 0.8825 (mt0) cc_final: 0.8598 (mt0) outliers start: 122 outliers final: 70 residues processed: 656 average time/residue: 0.8195 time to fit residues: 594.8768 Evaluate side-chains 673 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 587 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 434 PHE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 497 ARG Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 525 GLN Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 606 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 524 GLU Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 575 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 121 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 0.0970 chunk 267 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 142 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 409 HIS A 473 GLN A 546 ASN B 25 GLN B 282 ASN B 422 ASN B 465 ASN C 372 ASN C 409 HIS C 546 ASN D 239 HIS D 316 ASN D 355 ASN D 409 HIS D 515 GLN D 580 GLN E 355 ASN E 473 GLN E 546 ASN F 355 ASN F 409 HIS F 603 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100753 restraints weight = 33943.572| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.06 r_work: 0.3225 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22253 Z= 0.118 Angle : 0.533 12.390 30388 Z= 0.262 Chirality : 0.040 0.235 3385 Planarity : 0.004 0.055 3945 Dihedral : 9.073 107.011 3316 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.73 % Rotamer: Outliers : 5.62 % Allowed : 21.72 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.16), residues: 2721 helix: 1.57 (0.14), residues: 1334 sheet: -0.20 (0.32), residues: 270 loop : 0.05 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 290 TYR 0.013 0.001 TYR C 356 PHE 0.010 0.001 PHE C 476 TRP 0.014 0.001 TRP C 237 HIS 0.008 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (22235) covalent geometry : angle 0.53317 / 0.26 (30388) hydrogen bonds : bond 0.03367 / 2.20 ( 971) hydrogen bonds : angle 4.24643 / 3.06 ( 2751) metal coordination : bond 0.00156 / 0.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 599 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8784 (m) cc_final: 0.8546 (p) REVERT: A 28 ASP cc_start: 0.8143 (m-30) cc_final: 0.7631 (m-30) REVERT: A 29 GLU cc_start: 0.7394 (mp0) cc_final: 0.6808 (mp0) REVERT: A 114 ARG cc_start: 0.7783 (mtp85) cc_final: 0.7570 (ttm-80) REVERT: A 147 VAL cc_start: 0.8495 (t) cc_final: 0.8238 (p) REVERT: A 164 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8092 (mp0) REVERT: A 222 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7723 (pt) REVERT: A 240 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8021 (mm-30) REVERT: A 273 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8067 (tp) REVERT: A 324 ASP cc_start: 0.8247 (t0) cc_final: 0.8021 (t0) REVERT: A 376 GLN cc_start: 0.8273 (tp40) cc_final: 0.8038 (tt0) REVERT: A 379 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: A 418 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 496 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8368 (tp) REVERT: A 529 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8419 (mp0) REVERT: B 30 VAL cc_start: 0.8485 (t) cc_final: 0.8185 (p) REVERT: B 45 GLU cc_start: 0.8024 (tp30) cc_final: 0.7802 (tp30) REVERT: B 65 GLN cc_start: 0.7421 (tp40) cc_final: 0.6986 (tt0) REVERT: B 85 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7472 (mtt90) REVERT: B 160 ARG cc_start: 0.8312 (ptp-110) cc_final: 0.7985 (mtm110) REVERT: B 164 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 167 TRP cc_start: 0.8344 (m-10) cc_final: 0.7915 (m-10) REVERT: B 178 PHE cc_start: 0.7855 (m-80) cc_final: 0.7562 (m-80) REVERT: B 181 GLU cc_start: 0.8026 (mp0) cc_final: 0.7152 (mp0) REVERT: B 195 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7059 (p0) REVERT: B 245 VAL cc_start: 0.9209 (t) cc_final: 0.8968 (m) REVERT: B 279 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7867 (mt-10) REVERT: B 315 ASP cc_start: 0.8495 (m-30) cc_final: 0.8236 (m-30) REVERT: B 369 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7878 (mt-10) REVERT: B 376 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 403 ARG cc_start: 0.8084 (mmm160) cc_final: 0.7333 (mmm-85) REVERT: B 430 ASP cc_start: 0.8149 (t0) cc_final: 0.7924 (t0) REVERT: B 449 GLU cc_start: 0.7946 (tt0) cc_final: 0.7713 (tt0) REVERT: B 464 GLU cc_start: 0.7960 (tt0) cc_final: 0.7731 (tt0) REVERT: B 473 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8145 (mp10) REVERT: B 507 GLU cc_start: 0.8872 (mt-10) cc_final: 0.7457 (pt0) REVERT: B 552 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7909 (mt) REVERT: C 243 ASP cc_start: 0.8342 (t70) cc_final: 0.8035 (t0) REVERT: C 258 GLU cc_start: 0.7998 (tp30) cc_final: 0.7589 (tp30) REVERT: C 279 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8072 (mm-30) REVERT: C 315 ASP cc_start: 0.7979 (m-30) cc_final: 0.7641 (m-30) REVERT: C 324 ASP cc_start: 0.8030 (m-30) cc_final: 0.7803 (m-30) REVERT: C 342 ASP cc_start: 0.8129 (t70) cc_final: 0.7779 (t70) REVERT: C 379 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: C 418 GLU cc_start: 0.8032 (tp30) cc_final: 0.7801 (tp30) REVERT: C 430 ASP cc_start: 0.8438 (t70) cc_final: 0.8150 (t0) REVERT: C 461 HIS cc_start: 0.9204 (OUTLIER) cc_final: 0.8431 (m90) REVERT: C 467 ASP cc_start: 0.6121 (OUTLIER) cc_final: 0.5892 (p0) REVERT: C 491 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7887 (ttm-80) REVERT: C 497 ARG cc_start: 0.7640 (ttt180) cc_final: 0.7384 (ttt180) REVERT: C 522 ASP cc_start: 0.6688 (t0) cc_final: 0.6309 (t0) REVERT: C 556 SER cc_start: 0.8379 (t) cc_final: 0.8138 (t) REVERT: C 591 GLN cc_start: 0.8191 (tp40) cc_final: 0.7905 (tp40) REVERT: D 248 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7924 (tmmm) REVERT: D 290 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7406 (mtm-85) REVERT: D 307 LEU cc_start: 0.8414 (tm) cc_final: 0.7616 (tm) REVERT: D 311 MET cc_start: 0.8243 (mtm) cc_final: 0.7978 (mtm) REVERT: D 324 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8063 (t0) REVERT: D 342 ASP cc_start: 0.8606 (t0) cc_final: 0.8243 (t0) REVERT: D 418 GLU cc_start: 0.8014 (tt0) cc_final: 0.7765 (tm-30) REVERT: D 453 ARG cc_start: 0.8303 (tpp80) cc_final: 0.8069 (mmm160) REVERT: D 464 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5370 (tt0) REVERT: D 465 ASN cc_start: 0.5259 (OUTLIER) cc_final: 0.5002 (t0) REVERT: D 513 ASN cc_start: 0.9010 (m-40) cc_final: 0.8645 (m-40) REVERT: D 525 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7995 (pp30) REVERT: D 531 TYR cc_start: 0.8701 (t80) cc_final: 0.8491 (t80) REVERT: D 566 ARG cc_start: 0.8828 (mtp-110) cc_final: 0.8554 (mtp-110) REVERT: E 222 LEU cc_start: 0.8289 (mt) cc_final: 0.8072 (mt) REVERT: E 236 ARG cc_start: 0.8261 (mmt180) cc_final: 0.8014 (mtt180) REVERT: E 275 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8195 (mtmm) REVERT: E 279 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: E 333 ARG cc_start: 0.8280 (mtp85) cc_final: 0.8009 (mtp180) REVERT: E 342 ASP cc_start: 0.8688 (t70) cc_final: 0.8388 (t0) REVERT: E 449 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: E 525 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7421 (tm-30) REVERT: E 579 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8078 (p) REVERT: F 243 ASP cc_start: 0.8136 (m-30) cc_final: 0.7796 (m-30) REVERT: F 436 ASP cc_start: 0.7856 (t70) cc_final: 0.7311 (t0) REVERT: F 437 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7573 (mtm-85) REVERT: F 473 GLN cc_start: 0.8797 (mt0) cc_final: 0.8558 (mt0) REVERT: F 496 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8307 (tp) REVERT: F 523 GLU cc_start: 0.8065 (tp30) cc_final: 0.7861 (tp30) REVERT: F 525 GLN cc_start: 0.8221 (pm20) cc_final: 0.7977 (pm20) REVERT: F 575 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7643 (mp0) outliers start: 125 outliers final: 67 residues processed: 669 average time/residue: 0.8004 time to fit residues: 592.7124 Evaluate side-chains 674 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 588 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 434 PHE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 421 LYS Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 497 ARG Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 525 GLN Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 606 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 524 GLU Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 360 SER Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 575 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 145 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 409 HIS A 473 GLN A 580 GLN B 76 HIS B 282 ASN B 422 ASN B 461 HIS B 465 ASN C 546 ASN D 239 HIS D 355 ASN D 409 HIS D 515 GLN E 355 ASN E 549 ASN F 409 HIS F 515 GLN F 603 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097857 restraints weight = 34068.451| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.05 r_work: 0.3179 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22253 Z= 0.254 Angle : 0.615 11.820 30388 Z= 0.303 Chirality : 0.045 0.282 3385 Planarity : 0.005 0.059 3945 Dihedral : 8.890 108.436 3310 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.01 % Favored : 95.88 % Rotamer: Outliers : 5.31 % Allowed : 22.89 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 2721 helix: 1.34 (0.14), residues: 1336 sheet: -0.22 (0.32), residues: 270 loop : -0.04 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 385 TYR 0.012 0.002 TYR A 98 PHE 0.028 0.002 PHE B 125 TRP 0.022 0.002 TRP C 237 HIS 0.009 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.25 (22235) covalent geometry : angle 0.61461 / 0.30 (30388) hydrogen bonds : bond 0.04158 / 2.74 ( 971) hydrogen bonds : angle 4.39943 / 3.17 ( 2751) metal coordination : bond 0.00467 / 0.27 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 586 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8805 (m) cc_final: 0.8579 (p) REVERT: A 29 GLU cc_start: 0.7453 (mp0) cc_final: 0.6847 (mp0) REVERT: A 73 GLU cc_start: 0.7530 (mp0) cc_final: 0.7304 (mp0) REVERT: A 147 VAL cc_start: 0.8544 (t) cc_final: 0.8305 (p) REVERT: A 164 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8090 (mp0) REVERT: A 222 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7647 (pt) REVERT: A 240 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8015 (mm-30) REVERT: A 273 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8084 (tp) REVERT: A 376 GLN cc_start: 0.8295 (tp40) cc_final: 0.8063 (tt0) REVERT: A 379 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: A 405 ARG cc_start: 0.7318 (mtt90) cc_final: 0.7116 (mtt90) REVERT: A 418 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7718 (tm-30) REVERT: A 469 GLU cc_start: 0.8194 (tp30) cc_final: 0.7826 (tp30) REVERT: A 496 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 525 GLN cc_start: 0.8008 (mt0) cc_final: 0.7692 (mp10) REVERT: A 529 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8445 (mp0) REVERT: B 17 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7517 (mt-10) REVERT: B 30 VAL cc_start: 0.8498 (t) cc_final: 0.8173 (p) REVERT: B 45 GLU cc_start: 0.8081 (tp30) cc_final: 0.7688 (tp30) REVERT: B 160 ARG cc_start: 0.8318 (ptp-110) cc_final: 0.7895 (mtp85) REVERT: B 164 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 167 TRP cc_start: 0.8410 (m-10) cc_final: 0.7961 (m-10) REVERT: B 181 GLU cc_start: 0.8054 (mp0) cc_final: 0.7233 (mp0) REVERT: B 195 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7248 (p0) REVERT: B 213 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6223 (mm) REVERT: B 279 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7889 (mt-10) REVERT: B 315 ASP cc_start: 0.8507 (m-30) cc_final: 0.8255 (m-30) REVERT: B 369 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 418 GLU cc_start: 0.8344 (tp30) cc_final: 0.8041 (tp30) REVERT: B 449 GLU cc_start: 0.7912 (tt0) cc_final: 0.7693 (tt0) REVERT: B 464 GLU cc_start: 0.7918 (tt0) cc_final: 0.7684 (tt0) REVERT: B 473 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8173 (mp10) REVERT: B 507 GLU cc_start: 0.8950 (mt-10) cc_final: 0.7754 (pt0) REVERT: B 548 ASP cc_start: 0.7990 (t70) cc_final: 0.7580 (t0) REVERT: B 552 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8073 (mt) REVERT: C 243 ASP cc_start: 0.8331 (t70) cc_final: 0.8065 (t0) REVERT: C 258 GLU cc_start: 0.8068 (tp30) cc_final: 0.7629 (tp30) REVERT: C 279 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8056 (mm-30) REVERT: C 315 ASP cc_start: 0.8031 (m-30) cc_final: 0.7665 (m-30) REVERT: C 324 ASP cc_start: 0.8085 (m-30) cc_final: 0.7863 (m-30) REVERT: C 342 ASP cc_start: 0.8157 (t70) cc_final: 0.7817 (t70) REVERT: C 418 GLU cc_start: 0.8142 (tp30) cc_final: 0.7919 (tp30) REVERT: C 421 LYS cc_start: 0.8815 (mmmm) cc_final: 0.8595 (mmmm) REVERT: C 430 ASP cc_start: 0.8470 (t70) cc_final: 0.8183 (t0) REVERT: C 461 HIS cc_start: 0.9257 (OUTLIER) cc_final: 0.8495 (m90) REVERT: C 467 ASP cc_start: 0.6355 (OUTLIER) cc_final: 0.6080 (p0) REVERT: C 491 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.7990 (ttm-80) REVERT: C 497 ARG cc_start: 0.7672 (ttt180) cc_final: 0.7407 (ttt180) REVERT: C 522 ASP cc_start: 0.6839 (t0) cc_final: 0.6541 (t0) REVERT: C 556 SER cc_start: 0.8416 (t) cc_final: 0.8189 (t) REVERT: C 591 GLN cc_start: 0.8207 (tp40) cc_final: 0.7940 (tp40) REVERT: D 248 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7971 (tmmm) REVERT: D 290 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7474 (mtm-85) REVERT: D 307 LEU cc_start: 0.8485 (tm) cc_final: 0.7711 (tm) REVERT: D 311 MET cc_start: 0.8283 (mtm) cc_final: 0.8001 (mtm) REVERT: D 324 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8146 (t0) REVERT: D 342 ASP cc_start: 0.8589 (t0) cc_final: 0.8254 (t0) REVERT: D 418 GLU cc_start: 0.8061 (tt0) cc_final: 0.7816 (tm-30) REVERT: D 453 ARG cc_start: 0.8370 (tpp80) cc_final: 0.8096 (mmt90) REVERT: D 464 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.5446 (tt0) REVERT: D 465 ASN cc_start: 0.5217 (OUTLIER) cc_final: 0.4966 (t0) REVERT: D 513 ASN cc_start: 0.9018 (m-40) cc_final: 0.8600 (m-40) REVERT: D 525 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8000 (pp30) REVERT: D 531 TYR cc_start: 0.8735 (t80) cc_final: 0.8488 (t80) REVERT: E 222 LEU cc_start: 0.8463 (mt) cc_final: 0.8229 (mt) REVERT: E 236 ARG cc_start: 0.8304 (mmt180) cc_final: 0.8042 (mtt180) REVERT: E 275 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8524 (mtmm) REVERT: E 279 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: E 342 ASP cc_start: 0.8754 (t70) cc_final: 0.8419 (t0) REVERT: E 422 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8576 (p0) REVERT: E 449 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: E 525 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7479 (tm-30) REVERT: F 243 ASP cc_start: 0.8157 (m-30) cc_final: 0.7810 (m-30) REVERT: F 436 ASP cc_start: 0.7848 (t70) cc_final: 0.7306 (t0) REVERT: F 437 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7552 (mtm-85) REVERT: F 473 GLN cc_start: 0.8799 (mt0) cc_final: 0.8530 (mt0) REVERT: F 496 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8361 (tp) REVERT: F 523 GLU cc_start: 0.8120 (tp30) cc_final: 0.7654 (tp30) REVERT: F 525 GLN cc_start: 0.8214 (pm20) cc_final: 0.7732 (pm20) REVERT: F 575 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7587 (mp0) outliers start: 118 outliers final: 69 residues processed: 648 average time/residue: 0.8176 time to fit residues: 584.6181 Evaluate side-chains 653 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 565 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 497 ARG Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 525 GLN Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 606 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 524 GLU Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 575 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 53 optimal weight: 0.5980 chunk 192 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 0.0980 chunk 108 optimal weight: 0.9980 chunk 243 optimal weight: 0.5980 chunk 239 optimal weight: 0.9990 chunk 254 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 409 HIS A 473 GLN B 282 ASN B 422 ASN B 465 ASN C 355 ASN C 409 HIS C 546 ASN ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 355 ASN D 409 HIS D 515 GLN D 580 GLN E 368 GLN E 465 ASN E 546 ASN E 549 ASN F 409 HIS F 585 GLN F 603 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.113077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099678 restraints weight = 33820.852| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.06 r_work: 0.3212 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22253 Z= 0.137 Angle : 0.569 11.972 30388 Z= 0.280 Chirality : 0.041 0.224 3385 Planarity : 0.005 0.058 3945 Dihedral : 8.648 107.899 3305 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.42 % Favored : 96.51 % Rotamer: Outliers : 4.81 % Allowed : 23.16 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 2721 helix: 1.48 (0.14), residues: 1336 sheet: -0.24 (0.32), residues: 270 loop : 0.01 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 290 TYR 0.018 0.001 TYR C 356 PHE 0.024 0.001 PHE B 125 TRP 0.019 0.001 TRP C 237 HIS 0.009 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (22235) covalent geometry : angle 0.56877 / 0.28 (30388) hydrogen bonds : bond 0.03518 / 2.30 ( 971) hydrogen bonds : angle 4.27435 / 3.08 ( 2751) metal coordination : bond 0.00188 / 0.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 579 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8771 (m) cc_final: 0.8539 (p) REVERT: A 29 GLU cc_start: 0.7384 (mp0) cc_final: 0.6786 (mp0) REVERT: A 147 VAL cc_start: 0.8504 (t) cc_final: 0.8259 (p) REVERT: A 164 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8071 (mp0) REVERT: A 222 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7562 (pt) REVERT: A 240 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8039 (mm-30) REVERT: A 273 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8094 (tp) REVERT: A 285 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8594 (p) REVERT: A 376 GLN cc_start: 0.8251 (tp40) cc_final: 0.8021 (tt0) REVERT: A 379 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: A 418 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 473 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8505 (mt0) REVERT: A 496 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8366 (tp) REVERT: A 525 GLN cc_start: 0.8028 (mt0) cc_final: 0.7707 (mp10) REVERT: A 529 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8421 (mp0) REVERT: B 17 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 30 VAL cc_start: 0.8478 (t) cc_final: 0.8174 (p) REVERT: B 45 GLU cc_start: 0.8116 (tp30) cc_final: 0.7787 (tp30) REVERT: B 65 GLN cc_start: 0.7332 (tp40) cc_final: 0.7121 (tt0) REVERT: B 160 ARG cc_start: 0.8277 (ptp-110) cc_final: 0.8054 (mtm110) REVERT: B 167 TRP cc_start: 0.8413 (m-10) cc_final: 0.7963 (m-10) REVERT: B 195 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7302 (p0) REVERT: B 245 VAL cc_start: 0.9208 (t) cc_final: 0.8976 (m) REVERT: B 279 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7878 (mt-10) REVERT: B 315 ASP cc_start: 0.8512 (m-30) cc_final: 0.8240 (m-30) REVERT: B 369 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7928 (mt-10) REVERT: B 376 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 381 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8648 (t) REVERT: B 403 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7330 (mmm-85) REVERT: B 418 GLU cc_start: 0.8326 (tp30) cc_final: 0.7997 (tp30) REVERT: B 430 ASP cc_start: 0.8096 (t0) cc_final: 0.7815 (t0) REVERT: B 449 GLU cc_start: 0.7943 (tt0) cc_final: 0.7723 (tt0) REVERT: B 473 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8142 (mp10) REVERT: B 548 ASP cc_start: 0.8008 (t70) cc_final: 0.7591 (t0) REVERT: B 552 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7927 (mt) REVERT: B 593 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8135 (mt-10) REVERT: C 243 ASP cc_start: 0.8321 (t70) cc_final: 0.8088 (t0) REVERT: C 258 GLU cc_start: 0.8034 (tp30) cc_final: 0.7598 (tp30) REVERT: C 279 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 315 ASP cc_start: 0.7953 (m-30) cc_final: 0.7602 (m-30) REVERT: C 324 ASP cc_start: 0.8060 (m-30) cc_final: 0.7834 (m-30) REVERT: C 342 ASP cc_start: 0.8135 (t70) cc_final: 0.7788 (t70) REVERT: C 379 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: C 418 GLU cc_start: 0.8075 (tp30) cc_final: 0.7838 (tp30) REVERT: C 430 ASP cc_start: 0.8449 (t70) cc_final: 0.8166 (t0) REVERT: C 461 HIS cc_start: 0.9218 (OUTLIER) cc_final: 0.8423 (m90) REVERT: C 467 ASP cc_start: 0.6291 (p0) cc_final: 0.6008 (p0) REVERT: C 491 ARG cc_start: 0.8292 (ttm-80) cc_final: 0.7949 (ttm-80) REVERT: C 497 ARG cc_start: 0.7609 (ttt180) cc_final: 0.7305 (ttt90) REVERT: C 498 VAL cc_start: 0.7828 (t) cc_final: 0.7433 (p) REVERT: C 522 ASP cc_start: 0.6811 (t0) cc_final: 0.6514 (t0) REVERT: C 556 SER cc_start: 0.8396 (t) cc_final: 0.8155 (t) REVERT: C 591 GLN cc_start: 0.8203 (tp40) cc_final: 0.7968 (tp40) REVERT: D 248 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7946 (tmmm) REVERT: D 311 MET cc_start: 0.8257 (mtm) cc_final: 0.7979 (mtm) REVERT: D 324 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8138 (t0) REVERT: D 342 ASP cc_start: 0.8608 (t0) cc_final: 0.8247 (t0) REVERT: D 418 GLU cc_start: 0.8038 (tt0) cc_final: 0.7798 (tm-30) REVERT: D 453 ARG cc_start: 0.8347 (tpp80) cc_final: 0.8065 (mmt90) REVERT: D 464 GLU cc_start: 0.5702 (OUTLIER) cc_final: 0.5427 (tt0) REVERT: D 465 ASN cc_start: 0.5214 (OUTLIER) cc_final: 0.4956 (t0) REVERT: D 525 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7954 (pp30) REVERT: E 222 LEU cc_start: 0.8462 (mt) cc_final: 0.8227 (mt) REVERT: E 236 ARG cc_start: 0.8291 (mmt180) cc_final: 0.8005 (mtt180) REVERT: E 275 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8397 (mttm) REVERT: E 279 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: E 333 ARG cc_start: 0.8296 (mtp85) cc_final: 0.8061 (mtp85) REVERT: E 342 ASP cc_start: 0.8726 (t70) cc_final: 0.8411 (t0) REVERT: E 422 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8527 (p0) REVERT: E 449 GLU cc_start: 0.8333 (tt0) cc_final: 0.7921 (tt0) REVERT: E 525 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7436 (tm-30) REVERT: E 579 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8032 (p) REVERT: F 243 ASP cc_start: 0.8181 (m-30) cc_final: 0.7855 (m-30) REVERT: F 436 ASP cc_start: 0.7836 (t70) cc_final: 0.7286 (t0) REVERT: F 437 ARG cc_start: 0.8013 (mtm-85) cc_final: 0.7637 (mtm-85) REVERT: F 473 GLN cc_start: 0.8778 (mt0) cc_final: 0.8534 (mt0) REVERT: F 496 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8299 (tp) REVERT: F 523 GLU cc_start: 0.8142 (tp30) cc_final: 0.7932 (tp30) REVERT: F 525 GLN cc_start: 0.8231 (pm20) cc_final: 0.7986 (pm20) REVERT: F 575 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7532 (mp0) outliers start: 107 outliers final: 67 residues processed: 641 average time/residue: 0.8232 time to fit residues: 583.4483 Evaluate side-chains 663 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 575 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 497 ARG Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 525 GLN Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 606 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 524 GLU Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 575 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 270 optimal weight: 0.9990 chunk 231 optimal weight: 0.9990 chunk 29 optimal weight: 0.0770 chunk 230 optimal weight: 0.6980 chunk 173 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 251 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 210 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 409 HIS B 282 ASN B 422 ASN B 465 ASN C 355 ASN C 409 HIS ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 316 ASN D 355 ASN D 409 HIS D 515 GLN E 368 GLN F 409 HIS F 515 GLN F 546 ASN F 585 GLN F 603 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.113037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099687 restraints weight = 33891.034| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.06 r_work: 0.3211 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22253 Z= 0.147 Angle : 0.579 12.037 30388 Z= 0.285 Chirality : 0.042 0.248 3385 Planarity : 0.005 0.074 3945 Dihedral : 8.594 107.879 3305 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 4.72 % Allowed : 23.92 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 2721 helix: 1.47 (0.14), residues: 1341 sheet: -0.22 (0.32), residues: 269 loop : 0.04 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 290 TYR 0.009 0.001 TYR A 105 PHE 0.023 0.001 PHE B 125 TRP 0.019 0.001 TRP C 237 HIS 0.008 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (22235) covalent geometry : angle 0.57912 / 0.29 (30388) hydrogen bonds : bond 0.03577 / 2.34 ( 971) hydrogen bonds : angle 4.26066 / 3.07 ( 2751) metal coordination : bond 0.00245 / 0.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 579 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8779 (m) cc_final: 0.8554 (p) REVERT: A 29 GLU cc_start: 0.7404 (mp0) cc_final: 0.6785 (mp0) REVERT: A 140 GLU cc_start: 0.8344 (mp0) cc_final: 0.7884 (mm-30) REVERT: A 147 VAL cc_start: 0.8504 (t) cc_final: 0.8255 (p) REVERT: A 164 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8074 (mp0) REVERT: A 222 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7554 (pt) REVERT: A 240 GLU cc_start: 0.8249 (mt-10) cc_final: 0.8027 (mm-30) REVERT: A 273 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8105 (tp) REVERT: A 285 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8594 (p) REVERT: A 376 GLN cc_start: 0.8254 (tp40) cc_final: 0.8022 (tt0) REVERT: A 379 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: A 418 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 473 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8481 (mt0) REVERT: A 496 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8380 (tp) REVERT: A 525 GLN cc_start: 0.8000 (mt0) cc_final: 0.7700 (mp10) REVERT: A 529 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8458 (mp0) REVERT: B 2 ARG cc_start: 0.7663 (mpp80) cc_final: 0.7428 (mpp80) REVERT: B 30 VAL cc_start: 0.8474 (t) cc_final: 0.8162 (p) REVERT: B 45 GLU cc_start: 0.8096 (tp30) cc_final: 0.7759 (tp30) REVERT: B 65 GLN cc_start: 0.7361 (tp40) cc_final: 0.7091 (tt0) REVERT: B 73 GLU cc_start: 0.7620 (tt0) cc_final: 0.7310 (tt0) REVERT: B 160 ARG cc_start: 0.8268 (ptp-110) cc_final: 0.8043 (mtm110) REVERT: B 167 TRP cc_start: 0.8419 (m-10) cc_final: 0.7970 (m-10) REVERT: B 181 GLU cc_start: 0.7976 (mp0) cc_final: 0.7296 (mp0) REVERT: B 195 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7257 (p0) REVERT: B 236 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7611 (mtm-85) REVERT: B 245 VAL cc_start: 0.9208 (t) cc_final: 0.8976 (m) REVERT: B 279 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7897 (mt-10) REVERT: B 315 ASP cc_start: 0.8493 (m-30) cc_final: 0.8225 (m-30) REVERT: B 348 GLU cc_start: 0.8723 (mt-10) cc_final: 0.7442 (mt-10) REVERT: B 369 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 376 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 403 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7364 (mmm-85) REVERT: B 418 GLU cc_start: 0.8292 (tp30) cc_final: 0.8052 (tp30) REVERT: B 430 ASP cc_start: 0.8098 (t0) cc_final: 0.7794 (t0) REVERT: B 449 GLU cc_start: 0.7945 (tt0) cc_final: 0.7724 (tt0) REVERT: B 464 GLU cc_start: 0.8130 (tt0) cc_final: 0.7885 (tt0) REVERT: B 473 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8154 (mp10) REVERT: B 507 GLU cc_start: 0.8887 (mt-10) cc_final: 0.7917 (mp0) REVERT: B 548 ASP cc_start: 0.7995 (t70) cc_final: 0.7597 (t0) REVERT: B 552 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7960 (mt) REVERT: B 593 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7965 (mt-10) REVERT: C 243 ASP cc_start: 0.8336 (t70) cc_final: 0.8074 (t0) REVERT: C 258 GLU cc_start: 0.8064 (tp30) cc_final: 0.7620 (tp30) REVERT: C 279 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8032 (mm-30) REVERT: C 315 ASP cc_start: 0.7939 (m-30) cc_final: 0.7590 (m-30) REVERT: C 324 ASP cc_start: 0.8061 (m-30) cc_final: 0.7840 (m-30) REVERT: C 342 ASP cc_start: 0.8162 (t70) cc_final: 0.7814 (t70) REVERT: C 379 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: C 418 GLU cc_start: 0.8106 (tp30) cc_final: 0.7869 (tp30) REVERT: C 430 ASP cc_start: 0.8465 (t70) cc_final: 0.8183 (t0) REVERT: C 461 HIS cc_start: 0.9220 (OUTLIER) cc_final: 0.8417 (m90) REVERT: C 467 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.6013 (p0) REVERT: C 491 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.7980 (ttm-80) REVERT: C 497 ARG cc_start: 0.7633 (ttt180) cc_final: 0.7333 (ttt90) REVERT: C 522 ASP cc_start: 0.6862 (t0) cc_final: 0.6635 (t0) REVERT: C 556 SER cc_start: 0.8382 (t) cc_final: 0.8146 (t) REVERT: C 591 GLN cc_start: 0.8189 (tp40) cc_final: 0.7968 (tp40) REVERT: D 248 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7924 (tmmm) REVERT: D 324 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8139 (t0) REVERT: D 342 ASP cc_start: 0.8602 (t0) cc_final: 0.8245 (t0) REVERT: D 418 GLU cc_start: 0.8022 (tt0) cc_final: 0.7780 (tm-30) REVERT: D 453 ARG cc_start: 0.8371 (tpp80) cc_final: 0.8087 (mmt90) REVERT: D 464 GLU cc_start: 0.5665 (OUTLIER) cc_final: 0.5391 (tt0) REVERT: D 465 ASN cc_start: 0.5215 (OUTLIER) cc_final: 0.4970 (t0) REVERT: D 513 ASN cc_start: 0.9019 (m-40) cc_final: 0.8629 (m-40) REVERT: D 525 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7967 (pp30) REVERT: D 531 TYR cc_start: 0.8692 (t80) cc_final: 0.8465 (t80) REVERT: D 582 PHE cc_start: 0.8831 (m-10) cc_final: 0.8610 (m-80) REVERT: E 222 LEU cc_start: 0.8462 (mt) cc_final: 0.8227 (mt) REVERT: E 236 ARG cc_start: 0.8267 (mmt180) cc_final: 0.7990 (mtt180) REVERT: E 275 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8374 (mttm) REVERT: E 279 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: E 333 ARG cc_start: 0.8290 (mtp85) cc_final: 0.8052 (mtp85) REVERT: E 342 ASP cc_start: 0.8728 (t70) cc_final: 0.8408 (t0) REVERT: E 408 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7899 (mtt90) REVERT: E 422 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8576 (p0) REVERT: E 449 GLU cc_start: 0.8337 (tt0) cc_final: 0.7916 (tt0) REVERT: E 525 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7438 (tm-30) REVERT: F 243 ASP cc_start: 0.8163 (m-30) cc_final: 0.7834 (m-30) REVERT: F 436 ASP cc_start: 0.7825 (t70) cc_final: 0.7291 (t0) REVERT: F 437 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7643 (mtm-85) REVERT: F 473 GLN cc_start: 0.8778 (mt0) cc_final: 0.8538 (mt0) REVERT: F 496 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8324 (tp) REVERT: F 523 GLU cc_start: 0.8128 (tp30) cc_final: 0.7921 (tp30) REVERT: F 525 GLN cc_start: 0.8228 (pm20) cc_final: 0.7986 (pm20) REVERT: F 575 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7517 (mp0) outliers start: 105 outliers final: 71 residues processed: 641 average time/residue: 0.8195 time to fit residues: 580.4775 Evaluate side-chains 671 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 580 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 497 ARG Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 525 GLN Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 606 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 575 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 247 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 209 optimal weight: 0.8980 chunk 63 optimal weight: 0.0000 chunk 25 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 409 HIS A 473 GLN B 76 HIS B 422 ASN B 465 ASN C 355 ASN C 409 HIS ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS ** D 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 409 HIS D 515 GLN E 368 GLN E 546 ASN E 549 ASN F 409 HIS F 546 ASN F 585 GLN F 603 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100580 restraints weight = 33971.760| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.08 r_work: 0.3217 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22253 Z= 0.129 Angle : 0.572 12.010 30388 Z= 0.282 Chirality : 0.041 0.241 3385 Planarity : 0.005 0.061 3945 Dihedral : 8.490 107.509 3305 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 4.63 % Allowed : 23.92 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2721 helix: 1.55 (0.14), residues: 1339 sheet: -0.24 (0.32), residues: 269 loop : 0.06 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 290 TYR 0.019 0.001 TYR C 356 PHE 0.022 0.001 PHE B 125 TRP 0.020 0.001 TRP C 237 HIS 0.009 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (22235) covalent geometry : angle 0.57158 / 0.28 (30388) hydrogen bonds : bond 0.03402 / 2.23 ( 971) hydrogen bonds : angle 4.20915 / 3.03 ( 2751) metal coordination : bond 0.00164 / 0.10 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 582 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7355 (mtm180) cc_final: 0.7151 (mtm180) REVERT: A 11 SER cc_start: 0.8778 (m) cc_final: 0.8561 (p) REVERT: A 29 GLU cc_start: 0.7411 (mp0) cc_final: 0.6797 (mp0) REVERT: A 140 GLU cc_start: 0.8334 (mp0) cc_final: 0.7886 (mm-30) REVERT: A 147 VAL cc_start: 0.8502 (t) cc_final: 0.8239 (p) REVERT: A 164 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8120 (mp0) REVERT: A 208 ARG cc_start: 0.8394 (mtm110) cc_final: 0.8191 (mtm110) REVERT: A 219 ILE cc_start: 0.6572 (tt) cc_final: 0.6357 (tt) REVERT: A 222 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7634 (pt) REVERT: A 240 GLU cc_start: 0.8221 (mt-10) cc_final: 0.8003 (mm-30) REVERT: A 273 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8082 (tp) REVERT: A 379 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: A 418 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 496 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 525 GLN cc_start: 0.8011 (mt0) cc_final: 0.7713 (mp10) REVERT: B 30 VAL cc_start: 0.8481 (t) cc_final: 0.8168 (p) REVERT: B 45 GLU cc_start: 0.8116 (tp30) cc_final: 0.7730 (tp30) REVERT: B 73 GLU cc_start: 0.7627 (tt0) cc_final: 0.7332 (tt0) REVERT: B 160 ARG cc_start: 0.8241 (ptp-110) cc_final: 0.8033 (mtm110) REVERT: B 167 TRP cc_start: 0.8419 (m-10) cc_final: 0.7962 (m-10) REVERT: B 181 GLU cc_start: 0.7976 (mp0) cc_final: 0.7327 (mp0) REVERT: B 195 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7273 (p0) REVERT: B 236 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7601 (mtm-85) REVERT: B 245 VAL cc_start: 0.9197 (t) cc_final: 0.8972 (m) REVERT: B 279 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7912 (mt-10) REVERT: B 315 ASP cc_start: 0.8515 (m-30) cc_final: 0.8248 (m-30) REVERT: B 348 GLU cc_start: 0.8744 (mt-10) cc_final: 0.7574 (mt-10) REVERT: B 369 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8078 (mt-10) REVERT: B 376 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7859 (tm-30) REVERT: B 381 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8640 (t) REVERT: B 403 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7349 (mmm-85) REVERT: B 418 GLU cc_start: 0.8272 (tp30) cc_final: 0.8069 (tp30) REVERT: B 430 ASP cc_start: 0.8099 (t0) cc_final: 0.7764 (t0) REVERT: B 449 GLU cc_start: 0.7924 (tt0) cc_final: 0.7711 (tt0) REVERT: B 473 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8176 (mp10) REVERT: B 507 GLU cc_start: 0.8879 (mt-10) cc_final: 0.7948 (mp0) REVERT: B 548 ASP cc_start: 0.8008 (t70) cc_final: 0.7604 (t0) REVERT: B 552 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7930 (mt) REVERT: B 593 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7953 (mt-10) REVERT: C 243 ASP cc_start: 0.8339 (t70) cc_final: 0.8080 (t0) REVERT: C 258 GLU cc_start: 0.8096 (tp30) cc_final: 0.7638 (tp30) REVERT: C 279 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8019 (mm-30) REVERT: C 315 ASP cc_start: 0.7968 (m-30) cc_final: 0.7609 (m-30) REVERT: C 342 ASP cc_start: 0.8155 (t70) cc_final: 0.7823 (t70) REVERT: C 379 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: C 418 GLU cc_start: 0.8076 (tp30) cc_final: 0.7832 (tp30) REVERT: C 430 ASP cc_start: 0.8459 (t70) cc_final: 0.8172 (t0) REVERT: C 461 HIS cc_start: 0.9209 (OUTLIER) cc_final: 0.8390 (m90) REVERT: C 467 ASP cc_start: 0.6257 (OUTLIER) cc_final: 0.6003 (p0) REVERT: C 497 ARG cc_start: 0.7604 (ttt180) cc_final: 0.7258 (ttt180) REVERT: C 522 ASP cc_start: 0.6812 (t0) cc_final: 0.6575 (t0) REVERT: C 556 SER cc_start: 0.8335 (t) cc_final: 0.8111 (t) REVERT: C 591 GLN cc_start: 0.8207 (tp40) cc_final: 0.7987 (tp40) REVERT: D 248 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7919 (tmmm) REVERT: D 324 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8195 (t0) REVERT: D 342 ASP cc_start: 0.8613 (t0) cc_final: 0.8254 (t0) REVERT: D 418 GLU cc_start: 0.8035 (tt0) cc_final: 0.7780 (tm-30) REVERT: D 453 ARG cc_start: 0.8369 (tpp80) cc_final: 0.8009 (mmt90) REVERT: D 464 GLU cc_start: 0.5567 (OUTLIER) cc_final: 0.5330 (tt0) REVERT: D 465 ASN cc_start: 0.5207 (OUTLIER) cc_final: 0.4970 (t0) REVERT: D 513 ASN cc_start: 0.8999 (m-40) cc_final: 0.8600 (m-40) REVERT: D 525 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7986 (pp30) REVERT: D 531 TYR cc_start: 0.8690 (t80) cc_final: 0.8476 (t80) REVERT: E 222 LEU cc_start: 0.8436 (mt) cc_final: 0.8205 (mt) REVERT: E 236 ARG cc_start: 0.8294 (mmt180) cc_final: 0.8006 (mtt180) REVERT: E 275 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8516 (mtmm) REVERT: E 279 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: E 342 ASP cc_start: 0.8734 (t70) cc_final: 0.8423 (t0) REVERT: E 408 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7890 (mtt90) REVERT: E 422 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8526 (p0) REVERT: E 449 GLU cc_start: 0.8340 (tt0) cc_final: 0.7917 (tt0) REVERT: E 464 GLU cc_start: 0.8099 (tp30) cc_final: 0.7718 (tp30) REVERT: E 525 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7438 (tm-30) REVERT: E 579 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8067 (p) REVERT: F 243 ASP cc_start: 0.8155 (m-30) cc_final: 0.7827 (m-30) REVERT: F 436 ASP cc_start: 0.7798 (t70) cc_final: 0.7264 (t0) REVERT: F 437 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7636 (mtm-85) REVERT: F 473 GLN cc_start: 0.8777 (mt0) cc_final: 0.8545 (mt0) REVERT: F 496 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8317 (tp) REVERT: F 523 GLU cc_start: 0.8147 (tp30) cc_final: 0.7922 (tp30) REVERT: F 525 GLN cc_start: 0.8245 (pm20) cc_final: 0.8002 (pm20) REVERT: F 575 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7527 (mp0) outliers start: 103 outliers final: 69 residues processed: 641 average time/residue: 0.8311 time to fit residues: 589.4825 Evaluate side-chains 666 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 576 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 465 ASN Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 497 ARG Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 525 GLN Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 606 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain E residue 546 ASN Chi-restraints excluded: chain E residue 579 THR Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 461 HIS Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 575 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 64 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 258 optimal weight: 0.0020 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 409 HIS A 473 GLN B 76 HIS B 282 ASN B 422 ASN B 465 ASN C 355 ASN C 409 HIS ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** D 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN D 409 HIS D 515 GLN ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 ASN F 409 HIS F 515 GLN F 546 ASN F 591 GLN F 603 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.100421 restraints weight = 34085.094| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.08 r_work: 0.3214 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 22253 Z= 0.175 Angle : 0.732 59.162 30388 Z= 0.401 Chirality : 0.042 0.633 3385 Planarity : 0.005 0.061 3945 Dihedral : 8.488 107.515 3305 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 4.50 % Allowed : 24.51 % Favored : 71.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.17), residues: 2721 helix: 1.55 (0.14), residues: 1339 sheet: -0.23 (0.32), residues: 269 loop : 0.07 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 290 TYR 0.012 0.001 TYR C 356 PHE 0.021 0.001 PHE B 125 TRP 0.019 0.001 TRP C 237 HIS 0.007 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (22235) covalent geometry : angle 0.73250 / 0.40 (30388) hydrogen bonds : bond 0.03399 / 2.22 ( 971) hydrogen bonds : angle 4.20966 / 3.03 ( 2751) metal coordination : bond 0.00157 / 0.09 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11536.87 seconds wall clock time: 196 minutes 4.98 seconds (11764.98 seconds total)