Starting phenix.real_space_refine on Sat Jul 4 17:25:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w1f_65532/07_2026/9w1f_65532_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w1f_65532/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9w1f_65532/07_2026/9w1f_65532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w1f_65532/07_2026/9w1f_65532.map" model { file = "/net/cci-nas-00/data/ceres_data/9w1f_65532/07_2026/9w1f_65532_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w1f_65532/07_2026/9w1f_65532_trim.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 4.72, per 1000 atoms: 0.22 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: 1.73 Conformation dependent library (CDL) restraints added in 923.3 milliseconds 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: 0.81 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: 3.95 Time building geometry restraints manager: 2.33 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.480 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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= 0.230 Angle : 0.569 11.467 30388 Z= 0.323 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 : 0.608 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: 0.7404 time to fit residues: 664.9950 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 : 0.838 ------------------------------------------------------------------------------- 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... A 20 GLN A 89 GLN A 93 GLN A 169 GLN A 211 HIS A 278 GLN A 409 HIS 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 409 HIS 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 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 = 0.3556 r_free = 0.3556 target = 0.114139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100790 restraints weight = 33904.482| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.06 r_work: 0.3215 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22253 Z= 0.159 Angle : 0.584 12.875 30388 Z= 0.290 Chirality : 0.042 0.251 3385 Planarity : 0.005 0.060 3945 Dihedral : 10.637 106.693 3381 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 5.22 % Allowed : 16.28 % Favored : 78.51 % 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: 0.83 (0.16), residues: 2721 helix: 1.26 (0.14), residues: 1321 sheet: -0.01 (0.33), residues: 270 loop : -0.04 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 2 TYR 0.010 0.002 TYR C 356 PHE 0.019 0.001 PHE B 125 TRP 0.014 0.001 TRP E 364 HIS 0.008 0.001 HIS F 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (22235) covalent geometry : angle 0.58404 / 0.29 (30388) hydrogen bonds : bond 0.04566 / 2.99 ( 971) hydrogen bonds : angle 4.75243 / 3.44 ( 2751) metal coordination : bond 0.00279 / 0.15 ( 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 729 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 613 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8841 (m) cc_final: 0.8557 (p) REVERT: A 14 VAL cc_start: 0.8638 (m) cc_final: 0.8422 (t) REVERT: A 93 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7684 (mp-120) REVERT: A 147 VAL cc_start: 0.8474 (t) cc_final: 0.8179 (p) REVERT: A 219 ILE cc_start: 0.6778 (tt) cc_final: 0.6516 (tt) REVERT: A 222 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7524 (pt) REVERT: A 246 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7807 (mm-40) REVERT: A 273 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8064 (tp) REVERT: A 285 SER cc_start: 0.8907 (m) cc_final: 0.8617 (p) REVERT: A 319 SER cc_start: 0.8636 (p) cc_final: 0.8434 (t) REVERT: A 337 GLU cc_start: 0.8231 (tp30) cc_final: 0.8016 (tp30) REVERT: A 348 GLU cc_start: 0.8781 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 379 GLU cc_start: 0.8415 (tt0) cc_final: 0.8089 (mt-10) REVERT: A 396 THR cc_start: 0.8599 (p) cc_final: 0.8393 (m) REVERT: A 465 ASN cc_start: 0.8186 (m110) cc_final: 0.7883 (m-40) REVERT: A 507 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8276 (pt0) REVERT: A 523 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7270 (mm-30) REVERT: A 580 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8298 (mm110) REVERT: A 593 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8433 (mt-10) REVERT: B 17 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 164 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7817 (mm-30) REVERT: B 167 TRP cc_start: 0.8332 (m-10) cc_final: 0.7896 (m-10) REVERT: B 195 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7070 (p0) REVERT: B 279 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 303 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 315 ASP cc_start: 0.8382 (m-30) cc_final: 0.8012 (m-30) REVERT: B 348 GLU cc_start: 0.8726 (mt-10) cc_final: 0.7517 (mt-10) REVERT: B 369 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7988 (mt-10) REVERT: B 376 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7587 (tm-30) REVERT: B 449 GLU cc_start: 0.7825 (tt0) cc_final: 0.7531 (tt0) REVERT: B 456 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8410 (pt) REVERT: B 461 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.8154 (t70) REVERT: B 507 GLU cc_start: 0.8871 (mt-10) cc_final: 0.7677 (mt-10) REVERT: B 543 VAL cc_start: 0.8999 (p) cc_final: 0.8639 (t) REVERT: B 552 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8117 (mp) REVERT: B 557 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8282 (tt) REVERT: C 243 ASP cc_start: 0.8378 (t70) cc_final: 0.8104 (t0) REVERT: C 258 GLU cc_start: 0.8048 (tp30) cc_final: 0.7752 (tp30) REVERT: C 279 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7926 (mm-30) REVERT: C 315 ASP cc_start: 0.8511 (m-30) cc_final: 0.8159 (m-30) REVERT: C 342 ASP cc_start: 0.8057 (t70) cc_final: 0.7763 (t70) REVERT: C 418 GLU cc_start: 0.8049 (tp30) cc_final: 0.7768 (tp30) REVERT: C 421 LYS cc_start: 0.8781 (mmmm) cc_final: 0.8487 (mmmm) REVERT: C 430 ASP cc_start: 0.8392 (t70) cc_final: 0.8096 (t0) REVERT: C 461 HIS cc_start: 0.9117 (OUTLIER) cc_final: 0.8581 (m90) REVERT: C 467 ASP cc_start: 0.6258 (OUTLIER) cc_final: 0.5919 (p0) REVERT: C 553 SER cc_start: 0.8943 (m) cc_final: 0.8712 (m) REVERT: C 556 SER cc_start: 0.8467 (t) cc_final: 0.8178 (t) REVERT: C 566 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8126 (mtp-110) REVERT: C 571 ILE cc_start: 0.8383 (pt) cc_final: 0.8174 (pt) REVERT: C 591 GLN cc_start: 0.8187 (tp40) cc_final: 0.7870 (tp40) REVERT: D 245 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8587 (p) REVERT: D 278 GLN cc_start: 0.7434 (mt0) cc_final: 0.7068 (mt0) REVERT: D 290 ARG cc_start: 0.7144 (mmp-170) cc_final: 0.6938 (mmp-170) REVERT: D 302 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7435 (mm-30) REVERT: D 309 ARG cc_start: 0.8308 (mtm180) cc_final: 0.8061 (mtm180) REVERT: D 311 MET cc_start: 0.8302 (mtm) cc_final: 0.7997 (mtm) REVERT: D 386 ARG cc_start: 0.8802 (ttm170) cc_final: 0.8590 (ttm170) REVERT: D 418 GLU cc_start: 0.8125 (tt0) cc_final: 0.7868 (tm-30) REVERT: D 440 ARG cc_start: 0.7652 (ttm170) cc_final: 0.6846 (ttm170) REVERT: D 453 ARG cc_start: 0.8291 (tpp80) cc_final: 0.8076 (mmm160) REVERT: D 513 ASN cc_start: 0.8913 (m-40) cc_final: 0.8571 (m-40) REVERT: D 523 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: D 525 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8076 (pp30) REVERT: D 558 THR cc_start: 0.8471 (t) cc_final: 0.8215 (m) REVERT: E 222 LEU cc_start: 0.8236 (mt) cc_final: 0.7957 (mt) REVERT: E 236 ARG cc_start: 0.8376 (mmt180) cc_final: 0.8118 (mtt180) REVERT: E 279 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: E 329 ARG cc_start: 0.8121 (ttp-110) cc_final: 0.7675 (ttp-110) REVERT: E 333 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7929 (mtp180) REVERT: E 342 ASP cc_start: 0.8684 (t70) cc_final: 0.8369 (t0) REVERT: E 422 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8435 (p0) REVERT: E 554 GLN cc_start: 0.8918 (tt0) cc_final: 0.8675 (tt0) REVERT: F 243 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: F 302 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7664 (mm-30) REVERT: F 380 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: F 436 ASP cc_start: 0.7897 (t70) cc_final: 0.7475 (t0) REVERT: F 437 ARG cc_start: 0.7809 (mtm180) cc_final: 0.7548 (mtm-85) REVERT: F 465 ASN cc_start: 0.6469 (OUTLIER) cc_final: 0.6017 (m-40) REVERT: F 473 GLN cc_start: 0.8797 (mm110) cc_final: 0.8422 (mt0) REVERT: F 523 GLU cc_start: 0.8029 (tp30) cc_final: 0.7341 (tp30) REVERT: F 525 GLN cc_start: 0.8225 (pm20) cc_final: 0.7643 (pm20) REVERT: F 575 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: F 585 GLN cc_start: 0.8723 (mt0) cc_final: 0.8437 (mt0) outliers start: 116 outliers final: 50 residues processed: 679 average time/residue: 0.7977 time to fit residues: 601.2114 Evaluate side-chains 662 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 590 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 340 LEU 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 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 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 312 ARG 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 562 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 279 GLU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 422 ASN 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: 0.4980 chunk 115 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 HIS A 355 ASN 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 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN F 282 ASN F 409 HIS F 560 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099852 restraints weight = 34266.425| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.08 r_work: 0.3193 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22253 Z= 0.184 Angle : 0.569 12.135 30388 Z= 0.282 Chirality : 0.042 0.252 3385 Planarity : 0.005 0.052 3945 Dihedral : 9.998 106.896 3342 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 6.12 % Allowed : 17.99 % Favored : 75.90 % 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: 0.84 (0.16), residues: 2721 helix: 1.28 (0.14), residues: 1331 sheet: -0.09 (0.32), residues: 270 loop : -0.02 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 199 TYR 0.010 0.001 TYR E 531 PHE 0.014 0.001 PHE B 125 TRP 0.021 0.002 TRP C 237 HIS 0.007 0.001 HIS F 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 (22235) covalent geometry : angle 0.56851 / 0.28 (30388) hydrogen bonds : bond 0.04189 / 2.77 ( 971) hydrogen bonds : angle 4.57903 / 3.31 ( 2751) metal coordination : bond 0.00312 / 0.20 ( 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 752 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 616 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8828 (m) cc_final: 0.8554 (p) REVERT: A 28 ASP cc_start: 0.8132 (m-30) cc_final: 0.7869 (m-30) REVERT: A 71 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7787 (mmm-85) REVERT: A 123 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 147 VAL cc_start: 0.8471 (t) cc_final: 0.8256 (p) REVERT: A 164 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8258 (mm-30) REVERT: A 222 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7598 (pt) REVERT: A 273 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8048 (tp) REVERT: A 285 SER cc_start: 0.8881 (m) cc_final: 0.8578 (p) REVERT: A 319 SER cc_start: 0.8651 (p) cc_final: 0.8444 (t) REVERT: A 324 ASP cc_start: 0.8273 (t0) cc_final: 0.8073 (t0) REVERT: A 337 GLU cc_start: 0.8299 (tp30) cc_final: 0.8060 (tp30) REVERT: A 348 GLU cc_start: 0.8840 (mt-10) cc_final: 0.7830 (mt-10) REVERT: A 369 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 379 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: A 465 ASN cc_start: 0.8245 (m110) cc_final: 0.7910 (m-40) REVERT: A 496 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8355 (tp) REVERT: A 507 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8212 (pt0) REVERT: A 523 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7191 (mm-30) REVERT: A 525 GLN cc_start: 0.8195 (mt0) cc_final: 0.7971 (mt0) REVERT: A 534 ARG cc_start: 0.8949 (mmm-85) cc_final: 0.8557 (mtp85) REVERT: A 580 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8297 (mm110) REVERT: B 17 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 45 GLU cc_start: 0.8391 (tp30) cc_final: 0.8096 (tp30) REVERT: B 160 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.8050 (mtm-85) REVERT: B 164 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7841 (mm-30) REVERT: B 167 TRP cc_start: 0.8331 (m-10) cc_final: 0.7943 (m-10) REVERT: B 195 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7169 (p0) REVERT: B 203 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: B 279 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7962 (mt-10) REVERT: B 303 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8201 (mm-30) REVERT: B 315 ASP cc_start: 0.8430 (m-30) cc_final: 0.8170 (m-30) REVERT: B 369 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 376 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7572 (tm-30) REVERT: B 449 GLU cc_start: 0.7836 (tt0) cc_final: 0.7624 (tt0) REVERT: B 456 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8424 (pt) REVERT: B 461 HIS cc_start: 0.8576 (OUTLIER) cc_final: 0.8221 (t70) REVERT: B 507 GLU cc_start: 0.8913 (mt-10) cc_final: 0.7381 (pt0) REVERT: B 557 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8219 (tt) REVERT: C 243 ASP cc_start: 0.8404 (t70) cc_final: 0.8108 (t0) REVERT: C 258 GLU cc_start: 0.8071 (tp30) cc_final: 0.7681 (tp30) REVERT: C 279 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7988 (mm-30) REVERT: C 315 ASP cc_start: 0.8543 (m-30) cc_final: 0.8127 (m-30) REVERT: C 324 ASP cc_start: 0.8153 (m-30) cc_final: 0.7934 (m-30) REVERT: C 342 ASP cc_start: 0.8088 (t70) cc_final: 0.7767 (t70) REVERT: C 418 GLU cc_start: 0.8108 (tp30) cc_final: 0.7878 (tp30) REVERT: C 421 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8516 (mmmm) REVERT: C 430 ASP cc_start: 0.8442 (t70) cc_final: 0.8164 (t0) REVERT: C 461 HIS cc_start: 0.9157 (OUTLIER) cc_final: 0.8529 (m90) REVERT: C 467 ASP cc_start: 0.6272 (OUTLIER) cc_final: 0.5950 (p0) REVERT: C 495 LEU cc_start: 0.8008 (tm) cc_final: 0.7755 (tp) REVERT: C 522 ASP cc_start: 0.6831 (t0) cc_final: 0.6513 (t0) REVERT: C 556 SER cc_start: 0.8461 (t) cc_final: 0.8187 (t) REVERT: C 591 GLN cc_start: 0.8246 (tp40) cc_final: 0.7911 (tp40) REVERT: D 245 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8628 (p) REVERT: D 248 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7973 (tmmm) REVERT: D 278 GLN cc_start: 0.7456 (mt0) cc_final: 0.7149 (mt0) REVERT: D 290 ARG cc_start: 0.7176 (mmp-170) cc_final: 0.6878 (mmp-170) REVERT: D 311 MET cc_start: 0.8280 (mtm) cc_final: 0.7912 (mtm) REVERT: D 386 ARG cc_start: 0.8799 (ttm170) cc_final: 0.8585 (ttm170) REVERT: D 418 GLU cc_start: 0.8102 (tt0) cc_final: 0.7871 (tm-30) REVERT: D 453 ARG cc_start: 0.8287 (tpp80) cc_final: 0.8051 (mmm160) REVERT: D 464 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.5457 (tt0) REVERT: D 513 ASN cc_start: 0.8914 (m-40) cc_final: 0.8543 (m-40) REVERT: D 523 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: D 525 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8088 (pp30) REVERT: D 531 TYR cc_start: 0.8762 (t80) cc_final: 0.8561 (t80) REVERT: E 222 LEU cc_start: 0.8314 (mt) cc_final: 0.8080 (mt) REVERT: E 236 ARG cc_start: 0.8401 (mmt180) cc_final: 0.8133 (mtt180) REVERT: E 271 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7509 (mm-30) REVERT: E 279 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: E 329 ARG cc_start: 0.8169 (ttp-110) cc_final: 0.7752 (ttp-110) REVERT: E 342 ASP cc_start: 0.8734 (t70) cc_final: 0.8412 (t0) REVERT: E 464 GLU cc_start: 0.8237 (tt0) cc_final: 0.7939 (tp30) REVERT: E 495 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8572 (tt) REVERT: E 525 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7509 (tm-30) REVERT: E 554 GLN cc_start: 0.8936 (tt0) cc_final: 0.8733 (tt0) REVERT: F 243 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: F 302 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7757 (mm-30) REVERT: F 380 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: F 436 ASP cc_start: 0.7948 (t70) cc_final: 0.7457 (t0) REVERT: F 473 GLN cc_start: 0.8788 (mm110) cc_final: 0.8448 (mt0) REVERT: F 496 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8369 (tp) REVERT: F 523 GLU cc_start: 0.8083 (tp30) cc_final: 0.7327 (tp30) REVERT: F 525 GLN cc_start: 0.8241 (pm20) cc_final: 0.7624 (pm20) REVERT: F 575 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: F 585 GLN cc_start: 0.8799 (mt0) cc_final: 0.8565 (mt0) outliers start: 136 outliers final: 63 residues processed: 692 average time/residue: 0.7239 time to fit residues: 557.7943 Evaluate side-chains 674 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 587 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 71 ARG 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 379 GLU 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 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 203 GLU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 447 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 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 328 LEU 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 490 SER Chi-restraints excluded: chain C residue 507 GLU Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 303 GLU 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 479 SER 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 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 405 ARG Chi-restraints excluded: chain E residue 406 ILE 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 495 LEU Chi-restraints excluded: chain E residue 524 GLU Chi-restraints excluded: chain E residue 579 THR 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 383 GLU 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 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: 0.7980 chunk 166 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 222 optimal weight: 0.4980 chunk 160 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 170 optimal weight: 0.0050 chunk 35 optimal weight: 0.3980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 211 HIS A 316 ASN A 409 HIS B 282 ASN B 465 ASN C 375 GLN C 546 ASN D 409 HIS D 515 GLN D 546 ASN D 554 GLN E 317 ASN E 355 ASN E 546 ASN E 560 ASN F 409 HIS F 465 ASN F 560 ASN 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 = 0.113884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.100442 restraints weight = 33971.585| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.06 r_work: 0.3225 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22253 Z= 0.127 Angle : 0.542 12.378 30388 Z= 0.267 Chirality : 0.041 0.236 3385 Planarity : 0.005 0.054 3945 Dihedral : 9.690 106.326 3332 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.71 % Allowed : 19.69 % Favored : 74.60 % 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: 1.42 (0.14), residues: 1327 sheet: -0.11 (0.32), residues: 270 loop : -0.01 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 290 TYR 0.012 0.001 TYR C 356 PHE 0.011 0.001 PHE B 125 TRP 0.026 0.001 TRP C 237 HIS 0.007 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (22235) covalent geometry : angle 0.54195 / 0.27 (30388) hydrogen bonds : bond 0.03682 / 2.42 ( 971) hydrogen bonds : angle 4.42401 / 3.20 ( 2751) metal coordination : bond 0.00171 / 0.10 ( 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 721 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 594 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6607 (tmm) cc_final: 0.6371 (tmm) REVERT: A 11 SER cc_start: 0.8774 (m) cc_final: 0.8500 (p) REVERT: A 28 ASP cc_start: 0.8089 (m-30) cc_final: 0.7801 (m-30) REVERT: A 147 VAL cc_start: 0.8487 (t) cc_final: 0.8274 (p) REVERT: A 164 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8202 (mm-30) REVERT: A 222 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7620 (pt) REVERT: A 273 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8064 (tp) REVERT: A 285 SER cc_start: 0.8848 (m) cc_final: 0.8550 (p) REVERT: A 319 SER cc_start: 0.8642 (p) cc_final: 0.8421 (t) REVERT: A 324 ASP cc_start: 0.8258 (t0) cc_final: 0.8058 (t0) REVERT: A 337 GLU cc_start: 0.8327 (tp30) cc_final: 0.8067 (tp30) REVERT: A 348 GLU cc_start: 0.8847 (mt-10) cc_final: 0.7821 (mt-10) REVERT: A 379 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: A 465 ASN cc_start: 0.8232 (m110) cc_final: 0.7906 (m-40) REVERT: A 496 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8360 (tp) REVERT: A 507 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8204 (pt0) REVERT: A 523 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 525 GLN cc_start: 0.8196 (mt0) cc_final: 0.7974 (mt0) REVERT: A 534 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8461 (mtp85) REVERT: A 580 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8297 (mm110) REVERT: B 17 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7683 (mt-10) REVERT: B 45 GLU cc_start: 0.8288 (tp30) cc_final: 0.8058 (tp30) REVERT: B 160 ARG cc_start: 0.8351 (ptp-110) cc_final: 0.8000 (mtm-85) REVERT: B 164 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7746 (mm-30) REVERT: B 167 TRP cc_start: 0.8341 (m-10) cc_final: 0.7936 (m-10) REVERT: B 195 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7285 (p0) REVERT: B 279 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 315 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8154 (m-30) REVERT: B 369 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7888 (mt-10) REVERT: B 376 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7504 (tm-30) REVERT: B 381 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8752 (t) REVERT: B 449 GLU cc_start: 0.7850 (tt0) cc_final: 0.7629 (tt0) REVERT: B 461 HIS cc_start: 0.8553 (OUTLIER) cc_final: 0.8201 (t70) REVERT: B 507 GLU cc_start: 0.8891 (mt-10) cc_final: 0.7687 (pt0) REVERT: B 552 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7950 (mp) REVERT: B 557 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8208 (tt) REVERT: C 243 ASP cc_start: 0.8385 (t70) cc_final: 0.8039 (t0) REVERT: C 258 GLU cc_start: 0.8029 (tp30) cc_final: 0.7623 (tp30) REVERT: C 279 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7972 (mm-30) REVERT: C 315 ASP cc_start: 0.8334 (m-30) cc_final: 0.7962 (m-30) REVERT: C 324 ASP cc_start: 0.8148 (m-30) cc_final: 0.7932 (m-30) REVERT: C 342 ASP cc_start: 0.8118 (t70) cc_final: 0.7795 (t70) REVERT: C 418 GLU cc_start: 0.8043 (tp30) cc_final: 0.7800 (tp30) REVERT: C 430 ASP cc_start: 0.8415 (t70) cc_final: 0.8125 (t0) REVERT: C 461 HIS cc_start: 0.9197 (OUTLIER) cc_final: 0.8515 (m90) REVERT: C 467 ASP cc_start: 0.6135 (OUTLIER) cc_final: 0.5810 (p0) REVERT: C 522 ASP cc_start: 0.6839 (t0) cc_final: 0.6596 (t0) REVERT: C 556 SER cc_start: 0.8397 (t) cc_final: 0.8114 (t) REVERT: C 571 ILE cc_start: 0.8412 (pt) cc_final: 0.7917 (mt) REVERT: C 591 GLN cc_start: 0.8198 (tp40) cc_final: 0.7889 (tp40) REVERT: D 278 GLN cc_start: 0.7389 (mt0) cc_final: 0.7098 (mt0) REVERT: D 290 ARG cc_start: 0.7180 (mmp-170) cc_final: 0.6893 (mmp-170) REVERT: D 307 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7670 (tm) REVERT: D 311 MET cc_start: 0.8226 (mtm) cc_final: 0.7932 (mtm) REVERT: D 324 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8059 (t0) REVERT: D 342 ASP cc_start: 0.8632 (t0) cc_final: 0.8180 (t0) REVERT: D 378 MET cc_start: 0.8843 (mtm) cc_final: 0.8636 (mtp) REVERT: D 418 GLU cc_start: 0.8068 (tt0) cc_final: 0.7840 (tm-30) REVERT: D 453 ARG cc_start: 0.8274 (tpp80) cc_final: 0.8071 (mmm160) REVERT: D 464 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.5339 (tt0) REVERT: D 465 ASN cc_start: 0.5116 (OUTLIER) cc_final: 0.4863 (t0) REVERT: D 513 ASN cc_start: 0.8973 (m-40) cc_final: 0.8590 (m-40) REVERT: D 525 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8053 (pp30) REVERT: D 531 TYR cc_start: 0.8731 (t80) cc_final: 0.8513 (t80) REVERT: E 222 LEU cc_start: 0.8343 (mt) cc_final: 0.8118 (mt) REVERT: E 236 ARG cc_start: 0.8249 (mmt180) cc_final: 0.8041 (mtt180) REVERT: E 252 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8266 (tm-30) REVERT: E 271 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7494 (mm-30) REVERT: E 275 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8275 (mtmm) REVERT: E 279 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: E 329 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7724 (ttp-110) REVERT: E 342 ASP cc_start: 0.8719 (t70) cc_final: 0.8404 (t0) REVERT: E 449 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: E 464 GLU cc_start: 0.8249 (tt0) cc_final: 0.7953 (tp30) REVERT: E 525 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7459 (tm-30) REVERT: F 302 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7622 (mm-30) REVERT: F 436 ASP cc_start: 0.7953 (t70) cc_final: 0.7396 (t0) REVERT: F 465 ASN cc_start: 0.6736 (OUTLIER) cc_final: 0.6128 (m-40) REVERT: F 473 GLN cc_start: 0.8787 (mt0) cc_final: 0.8462 (mt0) REVERT: F 496 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8305 (tp) REVERT: F 523 GLU cc_start: 0.8021 (tp30) cc_final: 0.7313 (tp30) REVERT: F 525 GLN cc_start: 0.8212 (pm20) cc_final: 0.7637 (pm20) REVERT: F 575 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: F 585 GLN cc_start: 0.8791 (mt0) cc_final: 0.8571 (mt0) outliers start: 127 outliers final: 66 residues processed: 662 average time/residue: 0.7570 time to fit residues: 556.5093 Evaluate side-chains 662 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 573 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL 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 278 GLN 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 543 VAL Chi-restraints excluded: chain A residue 580 GLN 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 315 ASP 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 425 ARG 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 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 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 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 479 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 525 GLN Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 307 LEU 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 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 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 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 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 383 GLU 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 496 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 28 optimal weight: 0.0060 chunk 90 optimal weight: 0.0020 chunk 241 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 226 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 211 HIS A 409 HIS B 282 ASN B 419 HIS B 422 ASN B 465 ASN C 331 GLN C 372 ASN C 546 ASN D 355 ASN D 368 GLN D 409 HIS D 515 GLN E 316 ASN 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 = 0.3559 r_free = 0.3559 target = 0.114324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100859 restraints weight = 33970.197| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.08 r_work: 0.3222 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22253 Z= 0.128 Angle : 0.539 12.299 30388 Z= 0.265 Chirality : 0.041 0.236 3385 Planarity : 0.005 0.053 3945 Dihedral : 9.406 105.803 3320 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.66 % Rotamer: Outliers : 5.58 % Allowed : 21.13 % Favored : 73.29 % 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: 1.46 (0.14), residues: 1334 sheet: -0.12 (0.32), residues: 270 loop : 0.02 (0.19), residues: 1117 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 0.021 0.001 PHE A 67 TRP 0.013 0.001 TRP C 237 HIS 0.009 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (22235) covalent geometry : angle 0.53879 / 0.27 (30388) hydrogen bonds : bond 0.03540 / 2.32 ( 971) hydrogen bonds : angle 4.35536 / 3.15 ( 2751) metal coordination : bond 0.00201 / 0.13 ( 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 719 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 595 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6346 (tmm) REVERT: A 11 SER cc_start: 0.8785 (m) cc_final: 0.8513 (p) REVERT: A 28 ASP cc_start: 0.8115 (m-30) cc_final: 0.7818 (m-30) REVERT: A 73 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7158 (mt-10) REVERT: A 147 VAL cc_start: 0.8493 (t) cc_final: 0.8271 (p) REVERT: A 164 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8156 (mm-30) REVERT: A 222 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7674 (pt) REVERT: A 273 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8066 (tp) REVERT: A 285 SER cc_start: 0.8877 (m) cc_final: 0.8577 (p) REVERT: A 319 SER cc_start: 0.8665 (p) cc_final: 0.8438 (t) REVERT: A 324 ASP cc_start: 0.8284 (t0) cc_final: 0.8082 (t0) REVERT: A 337 GLU cc_start: 0.8339 (tp30) cc_final: 0.8077 (tp30) REVERT: A 348 GLU cc_start: 0.8867 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 379 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: A 465 ASN cc_start: 0.8251 (m110) cc_final: 0.7933 (m-40) REVERT: A 496 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 507 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8186 (pt0) REVERT: A 523 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 525 GLN cc_start: 0.8259 (mt0) cc_final: 0.8039 (mt0) REVERT: B 17 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7659 (mt-10) REVERT: B 30 VAL cc_start: 0.8499 (t) cc_final: 0.8181 (p) REVERT: B 160 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.7889 (mtm110) REVERT: B 164 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 167 TRP cc_start: 0.8331 (m-10) cc_final: 0.7895 (m-10) REVERT: B 195 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7329 (p0) REVERT: B 245 VAL cc_start: 0.9228 (t) cc_final: 0.8978 (m) REVERT: B 279 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7882 (mt-10) REVERT: B 315 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: B 358 SER cc_start: 0.8574 (t) cc_final: 0.8164 (p) REVERT: B 369 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 376 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7498 (tm-30) REVERT: B 381 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8726 (t) REVERT: B 430 ASP cc_start: 0.8192 (t0) cc_final: 0.7955 (t0) REVERT: B 437 ARG cc_start: 0.7858 (mmp80) cc_final: 0.7624 (mmp80) REVERT: B 449 GLU cc_start: 0.7855 (tt0) cc_final: 0.7634 (tt0) REVERT: B 461 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.8240 (t70) REVERT: B 507 GLU cc_start: 0.8896 (mt-10) cc_final: 0.7361 (pt0) REVERT: B 552 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7983 (mp) REVERT: C 243 ASP cc_start: 0.8299 (t70) cc_final: 0.7989 (p0) REVERT: C 258 GLU cc_start: 0.8063 (tp30) cc_final: 0.7646 (tp30) REVERT: C 279 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8021 (mm-30) REVERT: C 315 ASP cc_start: 0.8143 (m-30) cc_final: 0.7816 (m-30) REVERT: C 324 ASP cc_start: 0.8125 (m-30) cc_final: 0.7910 (m-30) REVERT: C 342 ASP cc_start: 0.8124 (t70) cc_final: 0.7779 (t70) REVERT: C 418 GLU cc_start: 0.8047 (tp30) cc_final: 0.7812 (tp30) REVERT: C 430 ASP cc_start: 0.8414 (t70) cc_final: 0.8121 (t0) REVERT: C 461 HIS cc_start: 0.9194 (OUTLIER) cc_final: 0.8487 (m90) REVERT: C 467 ASP cc_start: 0.6074 (OUTLIER) cc_final: 0.5761 (p0) REVERT: C 556 SER cc_start: 0.8400 (t) cc_final: 0.8152 (t) REVERT: C 591 GLN cc_start: 0.8205 (tp40) cc_final: 0.7920 (tp40) REVERT: D 307 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7607 (tm) REVERT: D 311 MET cc_start: 0.8206 (mtm) cc_final: 0.7907 (mtm) REVERT: D 324 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8059 (t0) REVERT: D 342 ASP cc_start: 0.8632 (t0) cc_final: 0.8180 (t0) REVERT: D 430 ASP cc_start: 0.8618 (t0) cc_final: 0.8416 (t0) REVERT: D 464 GLU cc_start: 0.5706 (OUTLIER) cc_final: 0.5402 (tt0) REVERT: D 465 ASN cc_start: 0.5092 (OUTLIER) cc_final: 0.4848 (t0) REVERT: D 513 ASN cc_start: 0.8978 (m-40) cc_final: 0.8626 (m-40) REVERT: D 525 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8071 (pp30) REVERT: D 531 TYR cc_start: 0.8714 (t80) cc_final: 0.8481 (t80) REVERT: E 222 LEU cc_start: 0.8319 (mt) cc_final: 0.8089 (mt) REVERT: E 236 ARG cc_start: 0.8228 (mmt180) cc_final: 0.8002 (mtt180) REVERT: E 271 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7432 (mm-30) REVERT: E 275 LYS cc_start: 0.8689 (mtpt) cc_final: 0.8193 (mtmm) REVERT: E 279 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: E 329 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7696 (ttp-110) REVERT: E 333 ARG cc_start: 0.8306 (mtp85) cc_final: 0.8049 (mtp180) REVERT: E 342 ASP cc_start: 0.8697 (t70) cc_final: 0.8386 (t0) REVERT: E 368 GLN cc_start: 0.8468 (mt0) cc_final: 0.8263 (mt0) REVERT: E 449 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: E 464 GLU cc_start: 0.8252 (tt0) cc_final: 0.7955 (tp30) REVERT: E 525 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7461 (tm-30) REVERT: F 243 ASP cc_start: 0.8078 (m-30) cc_final: 0.7727 (m-30) REVERT: F 436 ASP cc_start: 0.7895 (t70) cc_final: 0.7333 (t0) REVERT: F 437 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7803 (mtm-85) REVERT: F 473 GLN cc_start: 0.8795 (mt0) cc_final: 0.8466 (mt0) REVERT: F 496 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8333 (tp) REVERT: F 523 GLU cc_start: 0.8082 (tp30) cc_final: 0.7837 (tp30) REVERT: F 575 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: F 585 GLN cc_start: 0.8817 (mt0) cc_final: 0.8598 (mt0) outliers start: 124 outliers final: 68 residues processed: 667 average time/residue: 0.7606 time to fit residues: 565.0433 Evaluate side-chains 681 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 592 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 VAL 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 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 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 196 MET Chi-restraints excluded: chain B residue 315 ASP 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 425 ARG 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 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 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 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 473 GLN Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 307 LEU 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 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 550 LEU 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 235 LEU Chi-restraints excluded: chain E residue 279 GLU 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 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 383 GLU 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 564 THR Chi-restraints excluded: chain F residue 572 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: 1.9990 chunk 153 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 267 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 211 HIS A 409 HIS A 580 GLN B 54 HIS B 76 HIS B 282 ASN B 422 ASN B 465 ASN C 546 ASN D 355 ASN D 409 HIS D 515 GLN D 580 GLN E 316 ASN E 317 ASN E 355 ASN E 546 ASN F 409 HIS F 485 HIS F 546 ASN F 603 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100317 restraints weight = 33957.053| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.08 r_work: 0.3212 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2859 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= 0.157 Angle : 0.558 12.153 30388 Z= 0.274 Chirality : 0.042 0.248 3385 Planarity : 0.005 0.060 3945 Dihedral : 9.207 105.801 3315 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.44 % Rotamer: Outliers : 5.44 % Allowed : 21.58 % Favored : 72.98 % 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: 1.46 (0.14), residues: 1334 sheet: -0.14 (0.32), residues: 270 loop : 0.00 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 85 TYR 0.013 0.001 TYR C 356 PHE 0.027 0.001 PHE A 67 TRP 0.021 0.001 TRP C 237 HIS 0.008 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (22235) covalent geometry : angle 0.55758 / 0.27 (30388) hydrogen bonds : bond 0.03655 / 2.39 ( 971) hydrogen bonds : angle 4.34363 / 3.14 ( 2751) metal coordination : bond 0.00245 / 0.15 ( 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: 121 poor density : 603 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8786 (m) cc_final: 0.8518 (p) REVERT: A 28 ASP cc_start: 0.8131 (m-30) cc_final: 0.7828 (m-30) REVERT: A 71 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7775 (mmt180) REVERT: A 114 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7208 (ttp80) REVERT: A 140 GLU cc_start: 0.8363 (mp0) cc_final: 0.7980 (mm-30) REVERT: A 147 VAL cc_start: 0.8515 (t) cc_final: 0.8285 (p) REVERT: A 164 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8138 (mm-30) REVERT: A 222 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7682 (pt) REVERT: A 273 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8040 (tp) REVERT: A 285 SER cc_start: 0.8874 (m) cc_final: 0.8577 (p) REVERT: A 319 SER cc_start: 0.8674 (p) cc_final: 0.8448 (t) REVERT: A 324 ASP cc_start: 0.8335 (t0) cc_final: 0.8130 (t0) REVERT: A 337 GLU cc_start: 0.8357 (tp30) cc_final: 0.8098 (tp30) REVERT: A 369 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8104 (mt-10) REVERT: A 376 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: A 379 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: A 418 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7804 (tm-30) REVERT: A 435 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 465 ASN cc_start: 0.8256 (m110) cc_final: 0.7927 (m-40) REVERT: A 496 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8361 (tp) REVERT: A 525 GLN cc_start: 0.8221 (mt0) cc_final: 0.7747 (mt0) REVERT: B 17 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7624 (mt-10) REVERT: B 30 VAL cc_start: 0.8485 (t) cc_final: 0.8180 (p) REVERT: B 164 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7745 (mm-30) REVERT: B 167 TRP cc_start: 0.8341 (m-10) cc_final: 0.7902 (m-10) REVERT: B 181 GLU cc_start: 0.8092 (mp0) cc_final: 0.7078 (mp0) REVERT: B 195 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7381 (p0) REVERT: B 245 VAL cc_start: 0.9235 (t) cc_final: 0.8983 (m) REVERT: B 279 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 315 ASP cc_start: 0.8333 (m-30) cc_final: 0.8117 (m-30) REVERT: B 369 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7833 (mt-10) REVERT: B 381 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8699 (t) REVERT: B 430 ASP cc_start: 0.8169 (t0) cc_final: 0.7965 (t0) REVERT: B 437 ARG cc_start: 0.7868 (mmp80) cc_final: 0.7650 (mmp80) REVERT: B 449 GLU cc_start: 0.7896 (tt0) cc_final: 0.7664 (tt0) REVERT: B 464 GLU cc_start: 0.7954 (tt0) cc_final: 0.7712 (tt0) REVERT: B 507 GLU cc_start: 0.8918 (mt-10) cc_final: 0.7418 (pt0) REVERT: B 552 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7968 (mt) REVERT: C 243 ASP cc_start: 0.8299 (t70) cc_final: 0.7968 (p0) REVERT: C 258 GLU cc_start: 0.8039 (tp30) cc_final: 0.7626 (tp30) REVERT: C 279 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8012 (mm-30) REVERT: C 315 ASP cc_start: 0.8158 (m-30) cc_final: 0.7830 (m-30) REVERT: C 324 ASP cc_start: 0.8100 (m-30) cc_final: 0.7874 (m-30) REVERT: C 333 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7982 (mmm-85) REVERT: C 342 ASP cc_start: 0.8130 (t70) cc_final: 0.7801 (t70) REVERT: C 418 GLU cc_start: 0.8065 (tp30) cc_final: 0.7832 (tp30) REVERT: C 430 ASP cc_start: 0.8431 (t70) cc_final: 0.8143 (t0) REVERT: C 461 HIS cc_start: 0.9213 (OUTLIER) cc_final: 0.8478 (m90) REVERT: C 467 ASP cc_start: 0.6231 (OUTLIER) cc_final: 0.5983 (p0) REVERT: C 522 ASP cc_start: 0.6736 (t0) cc_final: 0.6356 (t0) REVERT: C 556 SER cc_start: 0.8411 (t) cc_final: 0.8167 (t) REVERT: C 591 GLN cc_start: 0.8198 (tp40) cc_final: 0.7916 (tp40) REVERT: D 307 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7665 (tm) REVERT: D 311 MET cc_start: 0.8220 (mtm) cc_final: 0.7944 (mtm) REVERT: D 324 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8083 (t0) REVERT: D 342 ASP cc_start: 0.8623 (t0) cc_final: 0.8239 (t0) REVERT: D 418 GLU cc_start: 0.8067 (tt0) cc_final: 0.7854 (tm-30) REVERT: D 430 ASP cc_start: 0.8630 (t0) cc_final: 0.8414 (t0) REVERT: D 453 ARG cc_start: 0.8363 (tpp80) cc_final: 0.8105 (mmm160) REVERT: D 464 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.5449 (tt0) REVERT: D 465 ASN cc_start: 0.5097 (OUTLIER) cc_final: 0.4832 (t0) REVERT: D 513 ASN cc_start: 0.8998 (m-40) cc_final: 0.8588 (m-40) REVERT: D 525 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8079 (pp30) REVERT: D 531 TYR cc_start: 0.8726 (t80) cc_final: 0.8521 (t80) REVERT: D 566 ARG cc_start: 0.8864 (mtp-110) cc_final: 0.8647 (mtp-110) REVERT: E 222 LEU cc_start: 0.8288 (mt) cc_final: 0.8055 (mt) REVERT: E 236 ARG cc_start: 0.8261 (mmt180) cc_final: 0.8024 (mtt180) REVERT: E 271 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7435 (mm-30) REVERT: E 275 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8194 (mtmm) REVERT: E 279 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: E 329 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7751 (ttp-110) REVERT: E 333 ARG cc_start: 0.8341 (mtp85) cc_final: 0.8074 (mtp180) REVERT: E 342 ASP cc_start: 0.8729 (t70) cc_final: 0.8410 (t0) REVERT: E 368 GLN cc_start: 0.8490 (mt0) cc_final: 0.8250 (mt0) REVERT: E 449 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: E 464 GLU cc_start: 0.8274 (tt0) cc_final: 0.7953 (tp30) REVERT: E 525 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7486 (tm-30) REVERT: F 243 ASP cc_start: 0.8122 (m-30) cc_final: 0.7790 (m-30) REVERT: F 302 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7732 (mm-30) REVERT: F 436 ASP cc_start: 0.7869 (t70) cc_final: 0.7320 (t0) REVERT: F 437 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7599 (mtm-85) REVERT: F 473 GLN cc_start: 0.8799 (mt0) cc_final: 0.8563 (mt0) REVERT: F 496 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8321 (tp) REVERT: F 523 GLU cc_start: 0.8102 (tp30) cc_final: 0.7862 (tp30) REVERT: F 525 GLN cc_start: 0.8268 (pm20) cc_final: 0.7984 (pm20) REVERT: F 575 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: F 585 GLN cc_start: 0.8853 (mt0) cc_final: 0.8606 (mt0) outliers start: 121 outliers final: 75 residues processed: 669 average time/residue: 0.7836 time to fit residues: 582.4507 Evaluate side-chains 683 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 589 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 VAL 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 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 376 GLN 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 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 87 LEU 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 335 LEU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 425 ARG Chi-restraints excluded: chain B residue 451 VAL 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 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 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 473 GLN Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 312 ARG 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 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 550 LEU 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 235 LEU Chi-restraints excluded: chain E residue 279 GLU 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 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 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 564 THR Chi-restraints excluded: chain F residue 572 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: 2.9990 chunk 154 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 HIS A 409 HIS A 546 ASN B 282 ASN B 422 ASN B 465 ASN C 409 HIS C 546 ASN D 316 ASN D 355 ASN D 409 HIS D 515 GLN E 355 ASN ** E 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN 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 = 0.3531 r_free = 0.3531 target = 0.112331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098863 restraints weight = 33929.624| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.05 r_work: 0.3196 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22253 Z= 0.209 Angle : 0.593 12.128 30388 Z= 0.290 Chirality : 0.043 0.266 3385 Planarity : 0.005 0.080 3945 Dihedral : 9.091 106.212 3313 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.53 % Favored : 96.36 % Rotamer: Outliers : 5.49 % Allowed : 22.35 % Favored : 72.17 % 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: 0.90 (0.16), residues: 2721 helix: 1.37 (0.14), residues: 1336 sheet: -0.16 (0.32), residues: 270 loop : -0.03 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 290 TYR 0.010 0.001 TYR C 356 PHE 0.029 0.002 PHE A 67 TRP 0.014 0.002 TRP C 237 HIS 0.008 0.001 HIS F 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (22235) covalent geometry : angle 0.59314 / 0.29 (30388) hydrogen bonds : bond 0.03867 / 2.54 ( 971) hydrogen bonds : angle 4.40067 / 3.17 ( 2751) metal coordination : bond 0.00418 / 0.28 ( 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 712 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 590 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8764 (m) cc_final: 0.8526 (p) REVERT: A 28 ASP cc_start: 0.8141 (m-30) cc_final: 0.7587 (m-30) REVERT: A 29 GLU cc_start: 0.7407 (mp0) cc_final: 0.6985 (mp0) REVERT: A 81 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: A 114 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7225 (ttp80) REVERT: A 140 GLU cc_start: 0.8334 (mp0) cc_final: 0.7964 (mm-30) REVERT: A 147 VAL cc_start: 0.8525 (t) cc_final: 0.8296 (p) REVERT: A 164 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8079 (mp0) REVERT: A 222 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7640 (pt) REVERT: A 240 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7933 (mm-30) REVERT: A 273 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8067 (tp) REVERT: A 285 SER cc_start: 0.8883 (m) cc_final: 0.8587 (p) REVERT: A 319 SER cc_start: 0.8690 (p) cc_final: 0.8460 (t) REVERT: A 324 ASP cc_start: 0.8373 (t0) cc_final: 0.8166 (t0) REVERT: A 376 GLN cc_start: 0.8308 (tp40) cc_final: 0.8070 (tt0) REVERT: A 379 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: A 418 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 435 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7554 (mt-10) REVERT: A 496 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8367 (tp) REVERT: A 529 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8429 (mp0) REVERT: B 30 VAL cc_start: 0.8490 (t) cc_final: 0.8175 (p) REVERT: B 164 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7725 (mm-30) REVERT: B 167 TRP cc_start: 0.8341 (m-10) cc_final: 0.7891 (m-10) REVERT: B 181 GLU cc_start: 0.8055 (mp0) cc_final: 0.7234 (mp0) REVERT: B 195 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7313 (p0) REVERT: B 245 VAL cc_start: 0.9221 (t) cc_final: 0.8973 (m) REVERT: B 279 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7888 (mt-10) REVERT: B 348 GLU cc_start: 0.8743 (mt-10) cc_final: 0.7396 (mt-10) REVERT: B 369 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7940 (mt-10) REVERT: B 381 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8685 (t) REVERT: B 437 ARG cc_start: 0.7878 (mmp80) cc_final: 0.7656 (mmp80) REVERT: B 449 GLU cc_start: 0.7922 (tt0) cc_final: 0.7690 (tt0) REVERT: B 464 GLU cc_start: 0.7949 (tt0) cc_final: 0.7710 (tt0) REVERT: B 473 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8171 (mp10) REVERT: B 507 GLU cc_start: 0.8932 (mt-10) cc_final: 0.7823 (pt0) REVERT: B 552 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8027 (mt) REVERT: C 243 ASP cc_start: 0.8320 (t70) cc_final: 0.8062 (t0) REVERT: C 258 GLU cc_start: 0.8072 (tp30) cc_final: 0.7647 (tp30) REVERT: C 279 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8006 (mm-30) REVERT: C 315 ASP cc_start: 0.8135 (m-30) cc_final: 0.7788 (m-30) REVERT: C 324 ASP cc_start: 0.8089 (m-30) cc_final: 0.7866 (m-30) REVERT: C 342 ASP cc_start: 0.8143 (t70) cc_final: 0.7803 (t70) REVERT: C 379 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: C 408 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8228 (mtt-85) REVERT: C 418 GLU cc_start: 0.8101 (tp30) cc_final: 0.7869 (tp30) REVERT: C 430 ASP cc_start: 0.8457 (t70) cc_final: 0.8166 (t0) REVERT: C 461 HIS cc_start: 0.9232 (OUTLIER) cc_final: 0.8478 (m90) REVERT: C 467 ASP cc_start: 0.6202 (OUTLIER) cc_final: 0.5980 (p0) REVERT: C 522 ASP cc_start: 0.6785 (t0) cc_final: 0.6388 (t0) REVERT: C 556 SER cc_start: 0.8403 (t) cc_final: 0.8124 (t) REVERT: C 591 GLN cc_start: 0.8189 (tp40) cc_final: 0.7915 (tp40) REVERT: D 307 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7684 (tm) REVERT: D 311 MET cc_start: 0.8233 (mtm) cc_final: 0.7954 (mtm) REVERT: D 324 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8091 (t0) REVERT: D 342 ASP cc_start: 0.8632 (t0) cc_final: 0.8250 (t0) REVERT: D 418 GLU cc_start: 0.8047 (tt0) cc_final: 0.7806 (tm-30) REVERT: D 453 ARG cc_start: 0.8326 (tpp80) cc_final: 0.7956 (tpp80) REVERT: D 464 GLU cc_start: 0.5712 (OUTLIER) cc_final: 0.5406 (tt0) REVERT: D 465 ASN cc_start: 0.5097 (OUTLIER) cc_final: 0.4827 (t0) REVERT: D 513 ASN cc_start: 0.9009 (m-40) cc_final: 0.8586 (m-40) REVERT: D 525 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8075 (pp30) REVERT: D 531 TYR cc_start: 0.8747 (t80) cc_final: 0.8530 (t80) REVERT: E 222 LEU cc_start: 0.8375 (mt) cc_final: 0.8120 (mt) REVERT: E 236 ARG cc_start: 0.8294 (mmt180) cc_final: 0.8047 (mtt180) REVERT: E 271 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7438 (mm-30) REVERT: E 275 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8407 (mtmm) REVERT: E 279 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: E 342 ASP cc_start: 0.8750 (t70) cc_final: 0.8420 (t0) REVERT: E 368 GLN cc_start: 0.8521 (mt0) cc_final: 0.8321 (mt0) REVERT: E 422 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8547 (p0) REVERT: E 449 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: E 464 GLU cc_start: 0.8269 (tt0) cc_final: 0.7937 (tp30) REVERT: E 525 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7443 (tm-30) REVERT: F 243 ASP cc_start: 0.8139 (m-30) cc_final: 0.7796 (m-30) REVERT: F 302 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7787 (mm-30) REVERT: F 436 ASP cc_start: 0.7876 (t70) cc_final: 0.7333 (t0) REVERT: F 437 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7646 (mtm-85) REVERT: F 473 GLN cc_start: 0.8805 (mt0) cc_final: 0.8573 (mt0) REVERT: F 496 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8349 (tp) REVERT: F 523 GLU cc_start: 0.8111 (tp30) cc_final: 0.7895 (tp30) REVERT: F 525 GLN cc_start: 0.8220 (pm20) cc_final: 0.7967 (pm20) REVERT: F 575 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: F 585 GLN cc_start: 0.8844 (mt0) cc_final: 0.8642 (mt0) outliers start: 122 outliers final: 80 residues processed: 656 average time/residue: 0.7724 time to fit residues: 562.8499 Evaluate side-chains 691 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 589 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 81 GLU 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 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 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 87 LEU 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 196 MET 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 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 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 379 GLU Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 408 ARG 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 507 GLU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 324 ASP Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 358 SER 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 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 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 233 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 337 GLU 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 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 E residue 601 LEU 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 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 Chi-restraints excluded: chain F residue 591 GLN 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: 0.5980 chunk 31 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 chunk 108 optimal weight: 0.5980 chunk 243 optimal weight: 0.7980 chunk 239 optimal weight: 2.9990 chunk 254 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 211 HIS A 409 HIS B 282 ASN B 422 ASN B 465 ASN C 355 ASN C 409 HIS C 546 ASN D 316 ASN D 355 ASN D 409 HIS D 515 GLN E 355 ASN ** E 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 549 ASN F 409 HIS F 546 ASN F 603 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.100087 restraints weight = 33824.598| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.07 r_work: 0.3206 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22253 Z= 0.141 Angle : 0.573 12.252 30388 Z= 0.282 Chirality : 0.041 0.265 3385 Planarity : 0.005 0.062 3945 Dihedral : 8.939 106.476 3310 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.42 % Favored : 96.47 % Rotamer: Outliers : 4.95 % Allowed : 22.66 % Favored : 72.39 % 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: 0.97 (0.16), residues: 2721 helix: 1.44 (0.14), residues: 1336 sheet: -0.19 (0.32), residues: 270 loop : 0.01 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 290 TYR 0.016 0.001 TYR C 356 PHE 0.030 0.001 PHE A 67 TRP 0.016 0.001 TRP C 237 HIS 0.008 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (22235) covalent geometry : angle 0.57273 / 0.28 (30388) hydrogen bonds : bond 0.03637 / 2.37 ( 971) hydrogen bonds : angle 4.31698 / 3.11 ( 2751) metal coordination : bond 0.00189 / 0.12 ( 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 702 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 592 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8764 (m) cc_final: 0.8515 (p) REVERT: A 28 ASP cc_start: 0.8125 (m-30) cc_final: 0.7534 (m-30) REVERT: A 29 GLU cc_start: 0.7384 (mp0) cc_final: 0.6987 (mp0) REVERT: A 81 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: A 114 ARG cc_start: 0.7552 (ttp80) cc_final: 0.7173 (ttp80) REVERT: A 140 GLU cc_start: 0.8316 (mp0) cc_final: 0.7974 (mm-30) REVERT: A 147 VAL cc_start: 0.8506 (t) cc_final: 0.8265 (p) REVERT: A 164 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8061 (mp0) REVERT: A 222 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7606 (pt) REVERT: A 240 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7925 (mm-30) REVERT: A 273 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8070 (tp) REVERT: A 285 SER cc_start: 0.8875 (m) cc_final: 0.8586 (p) REVERT: A 319 SER cc_start: 0.8691 (p) cc_final: 0.8442 (t) REVERT: A 324 ASP cc_start: 0.8307 (t0) cc_final: 0.8076 (t0) REVERT: A 376 GLN cc_start: 0.8278 (tp40) cc_final: 0.8053 (tt0) REVERT: A 379 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: A 418 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 435 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7784 (mt-10) REVERT: A 473 GLN cc_start: 0.8873 (mt0) cc_final: 0.8550 (mt0) REVERT: A 496 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 525 GLN cc_start: 0.7990 (mt0) cc_final: 0.7670 (mp10) REVERT: A 529 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8396 (mp0) REVERT: B 30 VAL cc_start: 0.8479 (t) cc_final: 0.8175 (p) REVERT: B 45 GLU cc_start: 0.8037 (tp30) cc_final: 0.7460 (tp30) REVERT: B 49 ARG cc_start: 0.7915 (mmt180) cc_final: 0.7362 (mmt180) REVERT: B 65 GLN cc_start: 0.7328 (tp-100) cc_final: 0.7087 (tt0) REVERT: B 140 GLU cc_start: 0.6769 (pm20) cc_final: 0.6512 (mp0) REVERT: B 164 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7776 (mm-30) REVERT: B 167 TRP cc_start: 0.8351 (m-10) cc_final: 0.7899 (m-10) REVERT: B 195 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7289 (p0) REVERT: B 245 VAL cc_start: 0.9211 (t) cc_final: 0.8970 (m) REVERT: B 279 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7839 (mt-10) REVERT: B 369 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7973 (mt-10) REVERT: B 403 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7403 (mmm-85) REVERT: B 430 ASP cc_start: 0.8127 (t0) cc_final: 0.7808 (t0) REVERT: B 437 ARG cc_start: 0.7885 (mmp80) cc_final: 0.7669 (mmp80) REVERT: B 449 GLU cc_start: 0.7937 (tt0) cc_final: 0.7708 (tt0) REVERT: B 454 VAL cc_start: 0.9057 (t) cc_final: 0.8766 (p) REVERT: B 473 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8172 (mp10) REVERT: B 552 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7969 (mt) REVERT: B 572 THR cc_start: 0.8056 (p) cc_final: 0.7732 (p) REVERT: B 593 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8119 (mt-10) REVERT: C 243 ASP cc_start: 0.8295 (t70) cc_final: 0.8037 (t0) REVERT: C 258 GLU cc_start: 0.8037 (tp30) cc_final: 0.7608 (tp30) REVERT: C 279 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8022 (mm-30) REVERT: C 315 ASP cc_start: 0.8086 (m-30) cc_final: 0.7752 (m-30) REVERT: C 324 ASP cc_start: 0.8072 (m-30) cc_final: 0.7852 (m-30) REVERT: C 342 ASP cc_start: 0.8162 (t70) cc_final: 0.7831 (t70) REVERT: C 379 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: C 418 GLU cc_start: 0.8140 (tp30) cc_final: 0.7907 (tp30) REVERT: C 430 ASP cc_start: 0.8443 (t70) cc_final: 0.8156 (t0) REVERT: C 461 HIS cc_start: 0.9223 (OUTLIER) cc_final: 0.8465 (m90) REVERT: C 467 ASP cc_start: 0.6321 (OUTLIER) cc_final: 0.6098 (p0) REVERT: C 491 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7915 (ttm-80) REVERT: C 522 ASP cc_start: 0.6783 (t0) cc_final: 0.6357 (t0) REVERT: C 556 SER cc_start: 0.8400 (t) cc_final: 0.8152 (t) REVERT: C 591 GLN cc_start: 0.8189 (tp40) cc_final: 0.7927 (tp40) REVERT: D 307 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7611 (tm) REVERT: D 311 MET cc_start: 0.8226 (mtm) cc_final: 0.7947 (mtm) REVERT: D 313 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8902 (mp) REVERT: D 324 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8077 (t0) REVERT: D 342 ASP cc_start: 0.8593 (t0) cc_final: 0.8223 (t0) REVERT: D 418 GLU cc_start: 0.8027 (tt0) cc_final: 0.7783 (tm-30) REVERT: D 453 ARG cc_start: 0.8308 (tpp80) cc_final: 0.8066 (mmm160) REVERT: D 464 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5372 (tt0) REVERT: D 465 ASN cc_start: 0.5206 (OUTLIER) cc_final: 0.4940 (t0) REVERT: D 513 ASN cc_start: 0.9005 (m-40) cc_final: 0.8645 (m-40) REVERT: D 525 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8009 (pp30) REVERT: E 222 LEU cc_start: 0.8386 (mt) cc_final: 0.8129 (mt) REVERT: E 236 ARG cc_start: 0.8330 (mmt180) cc_final: 0.8050 (mtt180) REVERT: E 271 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7400 (mm-30) REVERT: E 275 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8412 (mtmm) REVERT: E 279 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: E 333 ARG cc_start: 0.8308 (mtp85) cc_final: 0.8021 (mtp180) REVERT: E 342 ASP cc_start: 0.8733 (t70) cc_final: 0.8412 (t0) REVERT: E 368 GLN cc_start: 0.8525 (mt0) cc_final: 0.8312 (mt0) REVERT: E 422 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8539 (p0) REVERT: E 449 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: E 525 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7436 (tm-30) REVERT: F 243 ASP cc_start: 0.8140 (m-30) cc_final: 0.7797 (m-30) REVERT: F 302 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7728 (mm-30) REVERT: F 436 ASP cc_start: 0.7839 (t70) cc_final: 0.7298 (t0) REVERT: F 437 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7673 (mtm-85) REVERT: F 473 GLN cc_start: 0.8784 (mt0) cc_final: 0.8558 (mt0) REVERT: F 496 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8334 (tp) REVERT: F 523 GLU cc_start: 0.8123 (tp30) cc_final: 0.7896 (tp30) REVERT: F 525 GLN cc_start: 0.8212 (pm20) cc_final: 0.7962 (pm20) REVERT: F 575 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7593 (mp0) outliers start: 110 outliers final: 66 residues processed: 649 average time/residue: 0.7398 time to fit residues: 534.6633 Evaluate side-chains 676 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 589 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 81 GLU 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 273 LEU Chi-restraints excluded: chain A residue 278 GLN 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 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 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 328 LEU 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 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 579 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 313 LEU 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 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 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 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 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 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 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 564 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: 2.9990 chunk 231 optimal weight: 0.5980 chunk 29 optimal weight: 0.0020 chunk 230 optimal weight: 0.9990 chunk 173 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 251 optimal weight: 0.5980 chunk 189 optimal weight: 0.7980 chunk 210 optimal weight: 0.7980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 HIS A 409 HIS B 282 ASN B 422 ASN B 465 ASN C 355 ASN C 409 HIS C 546 ASN D 239 HIS D 316 ASN D 355 ASN D 409 HIS D 515 GLN E 355 ASN ** E 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 ASN F 409 HIS 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 = 0.3554 r_free = 0.3554 target = 0.113986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100601 restraints weight = 33894.273| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.06 r_work: 0.3223 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22253 Z= 0.120 Angle : 0.566 12.370 30388 Z= 0.278 Chirality : 0.041 0.241 3385 Planarity : 0.005 0.066 3945 Dihedral : 8.753 106.679 3308 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 4.32 % Allowed : 24.06 % Favored : 71.63 % 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: 1.06 (0.16), residues: 2721 helix: 1.52 (0.14), residues: 1336 sheet: -0.19 (0.33), residues: 270 loop : 0.05 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 290 TYR 0.008 0.001 TYR B 336 PHE 0.030 0.001 PHE A 67 TRP 0.018 0.001 TRP C 237 HIS 0.007 0.001 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (22235) covalent geometry : angle 0.56618 / 0.28 (30388) hydrogen bonds : bond 0.03397 / 2.21 ( 971) hydrogen bonds : angle 4.23902 / 3.06 ( 2751) metal coordination : bond 0.00139 / 0.09 ( 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 689 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 593 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8776 (m) cc_final: 0.8530 (p) REVERT: A 29 GLU cc_start: 0.7393 (mp0) cc_final: 0.6954 (mp0) REVERT: A 81 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: A 114 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7146 (ttp80) REVERT: A 140 GLU cc_start: 0.8302 (mp0) cc_final: 0.7935 (mm-30) REVERT: A 147 VAL cc_start: 0.8504 (t) cc_final: 0.8136 (p) REVERT: A 164 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8047 (mp0) REVERT: A 222 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7589 (pt) REVERT: A 240 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7967 (mm-30) REVERT: A 285 SER cc_start: 0.8856 (m) cc_final: 0.8560 (p) REVERT: A 319 SER cc_start: 0.8702 (p) cc_final: 0.8323 (m) REVERT: A 324 ASP cc_start: 0.8296 (t0) cc_final: 0.8059 (t0) REVERT: A 376 GLN cc_start: 0.8255 (tp40) cc_final: 0.8028 (tt0) REVERT: A 379 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: A 418 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 435 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7820 (mt-10) REVERT: A 496 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8369 (tp) REVERT: A 522 ASP cc_start: 0.8652 (m-30) cc_final: 0.8332 (m-30) REVERT: A 525 GLN cc_start: 0.8013 (mt0) cc_final: 0.7689 (mp10) REVERT: A 529 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8405 (mp0) REVERT: B 30 VAL cc_start: 0.8464 (t) cc_final: 0.8163 (p) REVERT: B 45 GLU cc_start: 0.8080 (tp30) cc_final: 0.7606 (tp30) REVERT: B 49 ARG cc_start: 0.7901 (mmt180) cc_final: 0.7469 (mmt180) REVERT: B 65 GLN cc_start: 0.7293 (tp-100) cc_final: 0.7065 (tt0) REVERT: B 73 GLU cc_start: 0.7591 (tt0) cc_final: 0.7247 (tt0) REVERT: B 160 ARG cc_start: 0.8235 (ptp-110) cc_final: 0.7931 (mtm-85) REVERT: B 164 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 167 TRP cc_start: 0.8329 (m-10) cc_final: 0.7863 (m-10) REVERT: B 181 GLU cc_start: 0.8025 (mp0) cc_final: 0.7286 (mp0) REVERT: B 195 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7233 (p0) REVERT: B 245 VAL cc_start: 0.9197 (t) cc_final: 0.8959 (m) REVERT: B 279 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 290 ARG cc_start: 0.8484 (ttp-110) cc_final: 0.8185 (mtp85) REVERT: B 348 GLU cc_start: 0.8739 (mt-10) cc_final: 0.7510 (mt-10) REVERT: B 369 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 376 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7925 (tm130) REVERT: B 403 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7407 (mmm-85) REVERT: B 430 ASP cc_start: 0.8122 (t0) cc_final: 0.7826 (t0) REVERT: B 449 GLU cc_start: 0.7893 (tt0) cc_final: 0.7687 (tt0) REVERT: B 464 GLU cc_start: 0.7930 (tt0) cc_final: 0.7709 (tt0) REVERT: B 473 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8165 (mp10) REVERT: B 507 GLU cc_start: 0.8886 (mt-10) cc_final: 0.7744 (pt0) REVERT: B 552 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7937 (mt) REVERT: C 243 ASP cc_start: 0.8278 (t70) cc_final: 0.8052 (t0) REVERT: C 258 GLU cc_start: 0.8058 (tp30) cc_final: 0.7616 (tp30) REVERT: C 279 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8043 (mm-30) REVERT: C 315 ASP cc_start: 0.8006 (m-30) cc_final: 0.7689 (m-30) REVERT: C 324 ASP cc_start: 0.8054 (m-30) cc_final: 0.7831 (m-30) REVERT: C 342 ASP cc_start: 0.8155 (t70) cc_final: 0.7819 (t70) REVERT: C 379 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: C 418 GLU cc_start: 0.8067 (tp30) cc_final: 0.7830 (tp30) REVERT: C 430 ASP cc_start: 0.8417 (t70) cc_final: 0.8139 (t0) REVERT: C 461 HIS cc_start: 0.9216 (OUTLIER) cc_final: 0.8435 (m90) REVERT: C 467 ASP cc_start: 0.6298 (p0) cc_final: 0.6081 (p0) REVERT: C 491 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7919 (ttm-80) REVERT: C 522 ASP cc_start: 0.6795 (t0) cc_final: 0.6478 (t0) REVERT: C 556 SER cc_start: 0.8388 (t) cc_final: 0.8146 (t) REVERT: C 591 GLN cc_start: 0.8198 (tp40) cc_final: 0.7934 (tp40) REVERT: D 313 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8879 (mp) REVERT: D 324 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8078 (t0) REVERT: D 342 ASP cc_start: 0.8586 (t0) cc_final: 0.8171 (t0) REVERT: D 418 GLU cc_start: 0.8034 (tt0) cc_final: 0.7768 (tm-30) REVERT: D 453 ARG cc_start: 0.8302 (tpp80) cc_final: 0.8026 (mmm-85) REVERT: D 464 GLU cc_start: 0.5673 (OUTLIER) cc_final: 0.5401 (tt0) REVERT: D 465 ASN cc_start: 0.5197 (OUTLIER) cc_final: 0.4933 (t0) REVERT: D 525 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8006 (pp30) REVERT: D 582 PHE cc_start: 0.8796 (m-10) cc_final: 0.8490 (m-80) REVERT: E 222 LEU cc_start: 0.8350 (mt) cc_final: 0.8094 (mt) REVERT: E 236 ARG cc_start: 0.8288 (mmt180) cc_final: 0.8012 (mtt180) REVERT: E 271 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7365 (mm-30) REVERT: E 275 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8288 (mtmm) REVERT: E 279 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: E 333 ARG cc_start: 0.8288 (mtp85) cc_final: 0.8066 (mtp85) REVERT: E 342 ASP cc_start: 0.8728 (t70) cc_final: 0.8415 (t0) REVERT: E 422 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8509 (p0) REVERT: E 449 GLU cc_start: 0.8314 (tt0) cc_final: 0.7889 (tt0) REVERT: E 525 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7442 (tm-30) REVERT: E 579 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8138 (p) REVERT: F 243 ASP cc_start: 0.8109 (m-30) cc_final: 0.7771 (m-30) REVERT: F 302 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7692 (mm-30) REVERT: F 436 ASP cc_start: 0.7842 (t70) cc_final: 0.7296 (t0) REVERT: F 437 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7635 (mtm-85) REVERT: F 473 GLN cc_start: 0.8781 (mt0) cc_final: 0.8559 (mt0) REVERT: F 496 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8301 (tp) REVERT: F 523 GLU cc_start: 0.8091 (tp30) cc_final: 0.7876 (tp30) REVERT: F 525 GLN cc_start: 0.8220 (pm20) cc_final: 0.7961 (pm20) REVERT: F 575 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7587 (mp0) outliers start: 96 outliers final: 64 residues processed: 645 average time/residue: 0.7779 time to fit residues: 557.7462 Evaluate side-chains 661 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 579 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 81 GLU 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 278 GLN 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 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 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 340 LEU 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 479 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 313 LEU 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 422 ASN 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 550 LEU 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 235 LEU Chi-restraints excluded: chain E residue 279 GLU 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 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 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 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: 0.8980 chunk 13 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 247 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 218 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 HIS A 409 HIS A 473 GLN B 422 ASN B 465 ASN C 355 ASN C 409 HIS D 316 ASN D 355 ASN D 409 HIS D 515 GLN E 355 ASN ** E 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 ASN F 515 GLN F 546 ASN F 603 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100086 restraints weight = 34047.604| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.07 r_work: 0.3218 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 22253 Z= 0.174 Angle : 0.745 59.199 30388 Z= 0.409 Chirality : 0.043 0.603 3385 Planarity : 0.005 0.138 3945 Dihedral : 8.671 106.626 3303 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 4.32 % Allowed : 23.74 % Favored : 71.94 % 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: 1.06 (0.16), residues: 2721 helix: 1.51 (0.14), residues: 1336 sheet: -0.19 (0.33), residues: 270 loop : 0.05 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG B 440 TYR 0.009 0.001 TYR D 356 PHE 0.028 0.001 PHE A 67 TRP 0.016 0.001 TRP C 237 HIS 0.007 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (22235) covalent geometry : angle 0.74464 / 0.41 (30388) hydrogen bonds : bond 0.03418 / 2.22 ( 971) hydrogen bonds : angle 4.24067 / 3.06 ( 2751) metal coordination : bond 0.00197 / 0.13 ( 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 670 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 574 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8773 (m) cc_final: 0.8529 (p) REVERT: A 29 GLU cc_start: 0.7287 (mp0) cc_final: 0.6945 (mp0) REVERT: A 81 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: A 114 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7170 (ttp80) REVERT: A 140 GLU cc_start: 0.8307 (mp0) cc_final: 0.7947 (mm-30) REVERT: A 147 VAL cc_start: 0.8501 (t) cc_final: 0.8251 (p) REVERT: A 164 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8056 (mp0) REVERT: A 222 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7593 (pt) REVERT: A 240 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7968 (mm-30) REVERT: A 285 SER cc_start: 0.8859 (m) cc_final: 0.8562 (p) REVERT: A 319 SER cc_start: 0.8694 (p) cc_final: 0.8313 (m) REVERT: A 376 GLN cc_start: 0.8263 (tp40) cc_final: 0.8036 (tt0) REVERT: A 379 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: A 418 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 435 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 496 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8388 (tp) REVERT: A 522 ASP cc_start: 0.8641 (m-30) cc_final: 0.8339 (m-30) REVERT: A 525 GLN cc_start: 0.8028 (mt0) cc_final: 0.7704 (mp10) REVERT: A 529 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8418 (mp0) REVERT: B 30 VAL cc_start: 0.8472 (t) cc_final: 0.8173 (p) REVERT: B 45 GLU cc_start: 0.8081 (tp30) cc_final: 0.7505 (tp30) REVERT: B 49 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7372 (mmt180) REVERT: B 65 GLN cc_start: 0.7307 (tp-100) cc_final: 0.7083 (tt0) REVERT: B 140 GLU cc_start: 0.6691 (pm20) cc_final: 0.6458 (mp0) REVERT: B 160 ARG cc_start: 0.8239 (ptp-110) cc_final: 0.7939 (mtm-85) REVERT: B 164 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7661 (mm-30) REVERT: B 167 TRP cc_start: 0.8327 (m-10) cc_final: 0.7897 (m-10) REVERT: B 195 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7253 (p0) REVERT: B 245 VAL cc_start: 0.9202 (t) cc_final: 0.8968 (m) REVERT: B 279 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7866 (mt-10) REVERT: B 369 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8089 (mt-10) REVERT: B 376 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7480 (tm-30) REVERT: B 403 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7409 (mmm-85) REVERT: B 430 ASP cc_start: 0.8129 (t0) cc_final: 0.7809 (t0) REVERT: B 449 GLU cc_start: 0.7888 (tt0) cc_final: 0.7683 (tt0) REVERT: B 461 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.8237 (t70) REVERT: B 464 GLU cc_start: 0.7923 (tt0) cc_final: 0.7703 (tt0) REVERT: B 473 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8182 (mp10) REVERT: B 552 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7945 (mt) REVERT: C 243 ASP cc_start: 0.8284 (t70) cc_final: 0.8040 (t0) REVERT: C 258 GLU cc_start: 0.8061 (tp30) cc_final: 0.7617 (tp30) REVERT: C 279 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 315 ASP cc_start: 0.8001 (m-30) cc_final: 0.7691 (m-30) REVERT: C 324 ASP cc_start: 0.8056 (m-30) cc_final: 0.7835 (m-30) REVERT: C 342 ASP cc_start: 0.8136 (t70) cc_final: 0.7800 (t70) REVERT: C 375 GLN cc_start: 0.8813 (tp40) cc_final: 0.8259 (tp-100) REVERT: C 379 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: C 418 GLU cc_start: 0.8056 (tp30) cc_final: 0.7819 (tp30) REVERT: C 430 ASP cc_start: 0.8428 (t70) cc_final: 0.8151 (t0) REVERT: C 461 HIS cc_start: 0.9217 (OUTLIER) cc_final: 0.8439 (m90) REVERT: C 467 ASP cc_start: 0.6283 (OUTLIER) cc_final: 0.6071 (p0) REVERT: C 491 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7911 (ttm-80) REVERT: C 522 ASP cc_start: 0.6791 (t0) cc_final: 0.6472 (t0) REVERT: C 556 SER cc_start: 0.8400 (t) cc_final: 0.8158 (t) REVERT: C 591 GLN cc_start: 0.8181 (tp40) cc_final: 0.7919 (tp40) REVERT: D 278 GLN cc_start: 0.7618 (mt0) cc_final: 0.7315 (mt0) REVERT: D 313 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8883 (mp) REVERT: D 324 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8075 (t0) REVERT: D 342 ASP cc_start: 0.8590 (t0) cc_final: 0.8176 (t0) REVERT: D 418 GLU cc_start: 0.8021 (tt0) cc_final: 0.7757 (tm-30) REVERT: D 453 ARG cc_start: 0.8310 (tpp80) cc_final: 0.8040 (mmt90) REVERT: D 464 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.5373 (tt0) REVERT: D 465 ASN cc_start: 0.5203 (OUTLIER) cc_final: 0.4941 (t0) REVERT: D 513 ASN cc_start: 0.8984 (m-40) cc_final: 0.8608 (m-40) REVERT: D 525 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7992 (pp30) REVERT: E 222 LEU cc_start: 0.8359 (mt) cc_final: 0.8104 (mt) REVERT: E 236 ARG cc_start: 0.8278 (mmt180) cc_final: 0.8012 (mtt180) REVERT: E 271 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7374 (mm-30) REVERT: E 275 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8300 (mtmm) REVERT: E 279 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: E 333 ARG cc_start: 0.8290 (mtp85) cc_final: 0.8071 (mtp85) REVERT: E 342 ASP cc_start: 0.8741 (t70) cc_final: 0.8433 (t0) REVERT: E 422 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8502 (p0) REVERT: E 449 GLU cc_start: 0.8330 (tt0) cc_final: 0.7900 (tt0) REVERT: E 525 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7429 (tm-30) REVERT: E 579 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8090 (p) REVERT: F 243 ASP cc_start: 0.8122 (m-30) cc_final: 0.7785 (m-30) REVERT: F 302 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7722 (mm-30) REVERT: F 436 ASP cc_start: 0.7838 (t70) cc_final: 0.7298 (t0) REVERT: F 437 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7640 (mtm-85) REVERT: F 473 GLN cc_start: 0.8783 (mt0) cc_final: 0.8561 (mt0) REVERT: F 496 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8299 (tp) REVERT: F 523 GLU cc_start: 0.8112 (tp30) cc_final: 0.7893 (tp30) REVERT: F 525 GLN cc_start: 0.8214 (pm20) cc_final: 0.7964 (pm20) REVERT: F 575 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7575 (mp0) outliers start: 96 outliers final: 65 residues processed: 625 average time/residue: 0.7650 time to fit residues: 531.3588 Evaluate side-chains 666 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 581 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 81 GLU 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 278 GLN 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 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 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 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 340 LEU 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 479 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 313 LEU 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 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 550 LEU 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 235 LEU Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 321 LEU 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 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 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 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: 0.7980 chunk 106 optimal weight: 0.5980 chunk 258 optimal weight: 2.9990 chunk 127 optimal weight: 0.0000 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 15 optimal weight: 0.0670 chunk 103 optimal weight: 0.8980 chunk 50 optimal weight: 0.0370 overall best weight: 0.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 HIS A 409 HIS A 473 GLN B 282 ASN B 388 HIS B 422 ASN B 465 ASN C 355 ASN C 409 HIS D 316 ASN D 355 ASN D 409 HIS ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 515 GLN E 355 ASN ** E 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 ASN F 546 ASN F 603 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100207 restraints weight = 34018.990| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.07 r_work: 0.3220 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 22253 Z= 0.174 Angle : 0.745 59.199 30388 Z= 0.409 Chirality : 0.043 0.603 3385 Planarity : 0.005 0.138 3945 Dihedral : 8.671 106.626 3303 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 3.96 % Allowed : 24.37 % Favored : 71.67 % 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: 1.06 (0.16), residues: 2721 helix: 1.51 (0.14), residues: 1336 sheet: -0.19 (0.33), residues: 270 loop : 0.05 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG B 440 TYR 0.009 0.001 TYR D 356 PHE 0.028 0.001 PHE A 67 TRP 0.016 0.001 TRP C 237 HIS 0.007 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (22235) covalent geometry : angle 0.74464 / 0.41 (30388) hydrogen bonds : bond 0.03418 / 2.22 ( 971) hydrogen bonds : angle 4.24067 / 3.06 ( 2751) metal coordination : bond 0.00197 / 0.13 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11235.05 seconds wall clock time: 191 minutes 6.46 seconds (11466.46 seconds total)