Starting phenix.real_space_refine on Thu Nov 20 11:21:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x6i_33022/11_2025/7x6i_33022_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x6i_33022/11_2025/7x6i_33022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x6i_33022/11_2025/7x6i_33022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x6i_33022/11_2025/7x6i_33022.map" model { file = "/net/cci-nas-00/data/ceres_data/7x6i_33022/11_2025/7x6i_33022_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x6i_33022/11_2025/7x6i_33022_trim.cif" } resolution = 3.93 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= 0.038 sd= 0.165 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 Ca 4 9.91 5 Zn 4 6.06 5 P 16 5.49 5 S 180 5.16 5 C 21256 2.51 5 N 5396 2.21 5 O 6008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32864 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5588 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 27, 'TRANS': 659} Chain breaks: 2 Chain: "E" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2480 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 3, 'TRANS': 301} Chain breaks: 1 Chain: "B" Number of atoms: 5588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5588 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 27, 'TRANS': 659} Chain breaks: 2 Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 116 Unusual residues: {' CA': 1, ' ZN': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1282 SG CYS A 176 49.195 110.784 101.540 1.00 99.11 S ATOM 1296 SG CYS A 178 45.896 110.787 99.609 1.00106.36 S ATOM 1318 SG CYS A 181 48.495 108.134 98.810 1.00 97.79 S ATOM 9350 SG CYS B 176 56.766 49.195 101.540 1.00 99.11 S ATOM 9364 SG CYS B 178 56.763 45.896 99.609 1.00106.36 S ATOM 9386 SG CYS B 181 59.416 48.495 98.810 1.00 97.79 S Restraints were copied for chains: D, C, F, G, H Time building chain proxies: 11.54, per 1000 atoms: 0.35 Number of scatterers: 32864 At special positions: 0 Unit cell: (168.64, 168.64, 177.344, 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 4 29.99 Ca 4 19.99 S 180 16.00 P 16 15.00 O 6008 8.00 N 5396 7.00 C 21256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 176 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 181 " pdb=" ZN B 803 " pdb="ZN ZN B 803 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 176 " pdb="ZN ZN B 803 " - pdb=" SG CYS B 181 " pdb=" ZN C 803 " pdb="ZN ZN C 803 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 803 " - pdb=" SG CYS C 181 " pdb=" ZN D 803 " pdb="ZN ZN D 803 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 176 " pdb="ZN ZN D 803 " - pdb=" SG CYS D 181 " Number of angles added : 12 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7616 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 8 sheets defined 70.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 58 removed outlier: 4.044A pdb=" N VAL A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.697A pdb=" N MET A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 4.162A pdb=" N TYR A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 118 removed outlier: 3.616A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.522A pdb=" N SER A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.804A pdb=" N ILE A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 401 through 424 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.832A pdb=" N ILE A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.359A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 3.528A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.614A pdb=" N ASN A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS A 553 " --> pdb=" O PRO A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 553' Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'A' and resid 615 through 632 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 636 through 648 Processing helix chain 'A' and resid 706 through 731 removed outlier: 3.617A pdb=" N ASN A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 753 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 62 through 69 removed outlier: 3.671A pdb=" N TYR E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.226A pdb=" N GLY E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 110 removed outlier: 3.749A pdb=" N ASP E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 132 Processing helix chain 'E' and resid 133 through 142 Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 151 through 158 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 204 through 215 removed outlier: 4.483A pdb=" N LYS E 209 " --> pdb=" O SER E 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS E 210 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE E 212 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS E 213 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE E 215 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 241 through 256 Processing helix chain 'E' and resid 257 through 260 removed outlier: 3.759A pdb=" N THR E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 257 through 260' Processing helix chain 'E' and resid 270 through 279 removed outlier: 4.163A pdb=" N LYS E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 328 through 347 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 58 removed outlier: 4.043A pdb=" N VAL B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.697A pdb=" N MET B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 4.162A pdb=" N TYR B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.616A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 removed outlier: 3.522A pdb=" N SER B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.804A pdb=" N ILE B 360 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 384 Processing helix chain 'B' and resid 401 through 424 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.832A pdb=" N ILE B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.359A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 3.528A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.614A pdb=" N ASN B 552 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS B 553 " --> pdb=" O PRO B 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 549 through 553' Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'B' and resid 615 through 632 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 636 through 648 Processing helix chain 'B' and resid 706 through 731 removed outlier: 3.617A pdb=" N ASN B 719 " --> pdb=" O GLU B 715 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 753 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 58 removed outlier: 4.043A pdb=" N VAL C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS C 49 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.697A pdb=" N MET C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 removed outlier: 4.162A pdb=" N TYR C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 118 removed outlier: 3.616A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 removed outlier: 3.522A pdb=" N SER C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.804A pdb=" N ILE C 360 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 401 through 424 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.832A pdb=" N ILE C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 4.359A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 3.528A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.614A pdb=" N ASN C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS C 553 " --> pdb=" O PRO C 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 549 through 553' Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 585 through 589 Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'C' and resid 615 through 632 Processing helix chain 'C' and resid 633 through 635 No H-bonds generated for 'chain 'C' and resid 633 through 635' Processing helix chain 'C' and resid 636 through 648 Processing helix chain 'C' and resid 706 through 731 removed outlier: 3.617A pdb=" N ASN C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 753 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 58 removed outlier: 4.043A pdb=" N VAL D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS D 49 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.697A pdb=" N MET D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 removed outlier: 4.162A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 118 removed outlier: 3.616A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 removed outlier: 3.522A pdb=" N SER D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.804A pdb=" N ILE D 360 " --> pdb=" O GLY D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 384 Processing helix chain 'D' and resid 401 through 424 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 426 through 431 removed outlier: 3.832A pdb=" N ILE D 431 " --> pdb=" O PHE D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 4.359A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 3.528A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.614A pdb=" N ASN D 552 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS D 553 " --> pdb=" O PRO D 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 549 through 553' Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 585 through 589 Processing helix chain 'D' and resid 594 through 615 Processing helix chain 'D' and resid 615 through 632 Processing helix chain 'D' and resid 633 through 635 No H-bonds generated for 'chain 'D' and resid 633 through 635' Processing helix chain 'D' and resid 636 through 648 Processing helix chain 'D' and resid 706 through 731 removed outlier: 3.617A pdb=" N ASN D 719 " --> pdb=" O GLU D 715 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 731 " --> pdb=" O ALA D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 753 Processing helix chain 'F' and resid 45 through 58 Processing helix chain 'F' and resid 62 through 69 removed outlier: 3.671A pdb=" N TYR F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.225A pdb=" N GLY F 89 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 removed outlier: 3.749A pdb=" N ASP F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 132 Processing helix chain 'F' and resid 133 through 142 Processing helix chain 'F' and resid 143 through 146 Processing helix chain 'F' and resid 151 through 158 Processing helix chain 'F' and resid 158 through 163 Processing helix chain 'F' and resid 170 through 176 Processing helix chain 'F' and resid 204 through 215 removed outlier: 4.483A pdb=" N LYS F 209 " --> pdb=" O SER F 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 210 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE F 212 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS F 213 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 215 " --> pdb=" O ILE F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 241 through 256 Processing helix chain 'F' and resid 257 through 260 removed outlier: 3.759A pdb=" N THR F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 257 through 260' Processing helix chain 'F' and resid 270 through 279 removed outlier: 4.162A pdb=" N LYS F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 286 Processing helix chain 'F' and resid 295 through 309 Processing helix chain 'F' and resid 328 through 347 Processing helix chain 'G' and resid 45 through 58 Processing helix chain 'G' and resid 62 through 69 removed outlier: 3.671A pdb=" N TYR G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.225A pdb=" N GLY G 89 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG G 90 " --> pdb=" O ARG G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 110 removed outlier: 3.749A pdb=" N ASP G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 132 Processing helix chain 'G' and resid 133 through 142 Processing helix chain 'G' and resid 143 through 146 Processing helix chain 'G' and resid 151 through 158 Processing helix chain 'G' and resid 158 through 163 Processing helix chain 'G' and resid 170 through 176 Processing helix chain 'G' and resid 204 through 215 removed outlier: 4.483A pdb=" N LYS G 209 " --> pdb=" O SER G 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS G 210 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE G 212 " --> pdb=" O LYS G 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS G 213 " --> pdb=" O LYS G 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE G 215 " --> pdb=" O ILE G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 230 No H-bonds generated for 'chain 'G' and resid 228 through 230' Processing helix chain 'G' and resid 241 through 256 Processing helix chain 'G' and resid 257 through 260 removed outlier: 3.759A pdb=" N THR G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 257 through 260' Processing helix chain 'G' and resid 270 through 279 removed outlier: 4.162A pdb=" N LYS G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 286 Processing helix chain 'G' and resid 295 through 309 Processing helix chain 'G' and resid 328 through 347 Processing helix chain 'H' and resid 45 through 58 Processing helix chain 'H' and resid 62 through 69 removed outlier: 3.671A pdb=" N TYR H 69 " --> pdb=" O GLU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.225A pdb=" N GLY H 89 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG H 90 " --> pdb=" O ARG H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 removed outlier: 3.749A pdb=" N ASP H 103 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 132 Processing helix chain 'H' and resid 133 through 142 Processing helix chain 'H' and resid 143 through 146 Processing helix chain 'H' and resid 151 through 158 Processing helix chain 'H' and resid 158 through 163 Processing helix chain 'H' and resid 170 through 176 Processing helix chain 'H' and resid 204 through 215 removed outlier: 4.483A pdb=" N LYS H 209 " --> pdb=" O SER H 206 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS H 210 " --> pdb=" O GLU H 207 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE H 212 " --> pdb=" O LYS H 209 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS H 213 " --> pdb=" O LYS H 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 215 " --> pdb=" O ILE H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 230 No H-bonds generated for 'chain 'H' and resid 228 through 230' Processing helix chain 'H' and resid 241 through 256 Processing helix chain 'H' and resid 257 through 260 removed outlier: 3.759A pdb=" N THR H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 257 through 260' Processing helix chain 'H' and resid 270 through 279 removed outlier: 4.162A pdb=" N LYS H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 286 Processing helix chain 'H' and resid 295 through 309 Processing helix chain 'H' and resid 328 through 347 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 removed outlier: 3.598A pdb=" N ILE B 168 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.602A pdb=" N ILE A 168 " --> pdb=" O ILE D 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL E 34 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE E 199 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU E 36 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL E 201 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU E 38 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS E 35 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE E 222 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU E 37 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N CYS E 224 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU E 39 " --> pdb=" O CYS E 224 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA E 226 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE E 264 " --> pdb=" O TYR E 320 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS E 322 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 266 " --> pdb=" O HIS E 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.600A pdb=" N ILE C 168 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 18 through 19 removed outlier: 3.600A pdb=" N ILE D 168 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL F 34 " --> pdb=" O LYS F 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE F 199 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU F 36 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL F 201 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS F 35 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE F 222 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU F 37 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N CYS F 224 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU F 39 " --> pdb=" O CYS F 224 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA F 226 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE F 264 " --> pdb=" O TYR F 320 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS F 322 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU F 266 " --> pdb=" O HIS F 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL G 34 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE G 199 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU G 36 " --> pdb=" O PHE G 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL G 201 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU G 38 " --> pdb=" O VAL G 201 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS G 35 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE G 222 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU G 37 " --> pdb=" O ILE G 222 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N CYS G 224 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU G 39 " --> pdb=" O CYS G 224 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA G 226 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE G 264 " --> pdb=" O TYR G 320 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS G 322 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU G 266 " --> pdb=" O HIS G 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 184 through 191 removed outlier: 6.408A pdb=" N VAL H 34 " --> pdb=" O LYS H 197 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE H 199 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU H 36 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL H 201 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU H 38 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS H 35 " --> pdb=" O ALA H 220 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE H 222 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU H 37 " --> pdb=" O ILE H 222 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N CYS H 224 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU H 39 " --> pdb=" O CYS H 224 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA H 226 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE H 264 " --> pdb=" O TYR H 320 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N HIS H 322 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU H 266 " --> pdb=" O HIS H 322 " (cutoff:3.500A) 1892 hydrogen bonds defined for protein. 5448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5746 1.32 - 1.45: 8730 1.45 - 1.58: 18748 1.58 - 1.70: 68 1.70 - 1.83: 284 Bond restraints: 33576 Sorted by residual: bond pdb=" C SER F 263 " pdb=" N ILE F 264 " ideal model delta sigma weight residual 1.329 1.447 -0.119 1.31e-02 5.83e+03 8.21e+01 bond pdb=" C SER G 263 " pdb=" N ILE G 264 " ideal model delta sigma weight residual 1.329 1.447 -0.119 1.31e-02 5.83e+03 8.21e+01 bond pdb=" C SER H 263 " pdb=" N ILE H 264 " ideal model delta sigma weight residual 1.329 1.447 -0.119 1.31e-02 5.83e+03 8.21e+01 bond pdb=" C SER E 263 " pdb=" N ILE E 264 " ideal model delta sigma weight residual 1.329 1.447 -0.119 1.31e-02 5.83e+03 8.21e+01 bond pdb=" CA VAL E 50 " pdb=" CB VAL E 50 " ideal model delta sigma weight residual 1.540 1.597 -0.057 1.25e-02 6.40e+03 2.08e+01 ... (remaining 33571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 42863 2.13 - 4.26: 2193 4.26 - 6.39: 240 6.39 - 8.52: 76 8.52 - 10.65: 48 Bond angle restraints: 45420 Sorted by residual: angle pdb=" C ASP E 133 " pdb=" N GLY E 134 " pdb=" CA GLY E 134 " ideal model delta sigma weight residual 120.00 111.68 8.32 1.10e+00 8.26e-01 5.72e+01 angle pdb=" C ASP F 133 " pdb=" N GLY F 134 " pdb=" CA GLY F 134 " ideal model delta sigma weight residual 120.00 111.72 8.28 1.10e+00 8.26e-01 5.66e+01 angle pdb=" C ASP G 133 " pdb=" N GLY G 134 " pdb=" CA GLY G 134 " ideal model delta sigma weight residual 120.00 111.72 8.28 1.10e+00 8.26e-01 5.66e+01 angle pdb=" C ASP H 133 " pdb=" N GLY H 134 " pdb=" CA GLY H 134 " ideal model delta sigma weight residual 120.00 111.72 8.28 1.10e+00 8.26e-01 5.66e+01 angle pdb=" O ASP F 133 " pdb=" C ASP F 133 " pdb=" N GLY F 134 " ideal model delta sigma weight residual 122.86 131.65 -8.79 1.18e+00 7.18e-01 5.54e+01 ... (remaining 45415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 19812 34.98 - 69.96: 504 69.96 - 104.93: 32 104.93 - 139.91: 28 139.91 - 174.89: 12 Dihedral angle restraints: 20388 sinusoidal: 8660 harmonic: 11728 Sorted by residual: dihedral pdb=" C8 GTP H 401 " pdb=" C1' GTP H 401 " pdb=" N9 GTP H 401 " pdb=" O4' GTP H 401 " ideal model delta sinusoidal sigma weight residual 104.59 -53.81 158.41 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C8 GTP G 401 " pdb=" C1' GTP G 401 " pdb=" N9 GTP G 401 " pdb=" O4' GTP G 401 " ideal model delta sinusoidal sigma weight residual 104.59 -53.81 158.41 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C8 GTP F 401 " pdb=" C1' GTP F 401 " pdb=" N9 GTP F 401 " pdb=" O4' GTP F 401 " ideal model delta sinusoidal sigma weight residual 104.59 -53.81 158.41 1 2.00e+01 2.50e-03 4.63e+01 ... (remaining 20385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4147 0.077 - 0.154: 746 0.154 - 0.232: 159 0.232 - 0.309: 16 0.309 - 0.386: 12 Chirality restraints: 5080 Sorted by residual: chirality pdb=" CA GLU G 58 " pdb=" N GLU G 58 " pdb=" C GLU G 58 " pdb=" CB GLU G 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA GLU H 58 " pdb=" N GLU H 58 " pdb=" C GLU H 58 " pdb=" CB GLU H 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA GLU F 58 " pdb=" N GLU F 58 " pdb=" C GLU F 58 " pdb=" CB GLU F 58 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 5077 not shown) Planarity restraints: 5652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 YZY B 805 " -0.088 2.00e-02 2.50e+03 8.76e-02 7.68e+01 pdb=" C28 YZY B 805 " 0.087 2.00e-02 2.50e+03 pdb=" C29 YZY B 805 " 0.088 2.00e-02 2.50e+03 pdb=" C30 YZY B 805 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY C 805 " -0.088 2.00e-02 2.50e+03 8.76e-02 7.68e+01 pdb=" C28 YZY C 805 " 0.087 2.00e-02 2.50e+03 pdb=" C29 YZY C 805 " 0.088 2.00e-02 2.50e+03 pdb=" C30 YZY C 805 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY A 806 " -0.088 2.00e-02 2.50e+03 8.76e-02 7.68e+01 pdb=" C28 YZY A 806 " 0.087 2.00e-02 2.50e+03 pdb=" C29 YZY A 806 " 0.088 2.00e-02 2.50e+03 pdb=" C30 YZY A 806 " -0.088 2.00e-02 2.50e+03 ... (remaining 5649 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 9220 2.82 - 3.34: 31875 3.34 - 3.86: 54356 3.86 - 4.38: 61661 4.38 - 4.90: 106218 Nonbonded interactions: 263330 Sorted by model distance: nonbonded pdb=" O ILE D 209 " pdb=" OG SER D 213 " model vdw 2.306 3.040 nonbonded pdb=" O ILE A 209 " pdb=" OG SER A 213 " model vdw 2.306 3.040 nonbonded pdb=" O ILE B 209 " pdb=" OG SER B 213 " model vdw 2.306 3.040 nonbonded pdb=" O ILE C 209 " pdb=" OG SER C 213 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.315 3.040 ... (remaining 263325 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 16 through 804) selection = (chain 'B' and resid 16 through 804) selection = (chain 'C' and resid 16 through 804) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 2.970 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: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 36.130 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 : 0.008 0.119 33596 Z= 0.483 Angle : 1.056 10.648 45440 Z= 0.626 Chirality : 0.066 0.386 5080 Planarity : 0.007 0.088 5652 Dihedral : 16.754 174.890 12760 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.45 % Allowed : 2.37 % Favored : 97.18 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.12), residues: 3928 helix: 0.10 (0.09), residues: 2516 sheet: -1.41 (0.48), residues: 116 loop : -0.81 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG G 176 TYR 0.024 0.003 TYR G 155 PHE 0.051 0.003 PHE D 540 TRP 0.048 0.002 TRP A 327 HIS 0.006 0.001 HIS E 322 Details of bonding type rmsd covalent geometry : bond 0.00833 (33576) covalent geometry : angle 1.05642 (45420) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.61058 ( 8) hydrogen bonds : bond 0.15985 ( 1892) hydrogen bonds : angle 5.98979 ( 5448) metal coordination : bond 0.00428 ( 16) metal coordination : angle 1.33372 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 516 time to evaluate : 1.254 Fit side-chains REVERT: A 66 MET cc_start: 0.7898 (mmm) cc_final: 0.7538 (tpt) REVERT: A 87 GLU cc_start: 0.8208 (tp30) cc_final: 0.7688 (tp30) REVERT: A 88 LEU cc_start: 0.9431 (tp) cc_final: 0.9224 (tp) REVERT: A 90 LEU cc_start: 0.9328 (tp) cc_final: 0.8987 (tp) REVERT: A 636 ASP cc_start: 0.8399 (t70) cc_final: 0.8169 (t0) REVERT: E 57 HIS cc_start: 0.6041 (m90) cc_final: 0.5592 (m170) REVERT: E 240 MET cc_start: 0.7488 (tpt) cc_final: 0.6875 (tpt) REVERT: E 243 MET cc_start: 0.7446 (tpp) cc_final: 0.6897 (tpp) REVERT: E 258 TRP cc_start: 0.7825 (m100) cc_final: 0.7154 (m100) REVERT: E 286 CYS cc_start: 0.7511 (t) cc_final: 0.7156 (t) REVERT: B 66 MET cc_start: 0.7900 (mmm) cc_final: 0.7534 (tpt) REVERT: B 87 GLU cc_start: 0.8211 (tp30) cc_final: 0.7691 (tp30) REVERT: B 88 LEU cc_start: 0.9427 (tp) cc_final: 0.9220 (tp) REVERT: B 90 LEU cc_start: 0.9327 (tp) cc_final: 0.8986 (tp) REVERT: B 636 ASP cc_start: 0.8403 (t70) cc_final: 0.8169 (t0) REVERT: C 66 MET cc_start: 0.7906 (mmm) cc_final: 0.7542 (tpt) REVERT: C 87 GLU cc_start: 0.8205 (tp30) cc_final: 0.7690 (tp30) REVERT: C 88 LEU cc_start: 0.9430 (tp) cc_final: 0.9224 (tp) REVERT: C 90 LEU cc_start: 0.9332 (tp) cc_final: 0.8985 (tp) REVERT: C 636 ASP cc_start: 0.8403 (t70) cc_final: 0.8171 (t0) REVERT: D 66 MET cc_start: 0.7896 (mmm) cc_final: 0.7532 (tpt) REVERT: D 87 GLU cc_start: 0.8215 (tp30) cc_final: 0.7693 (tp30) REVERT: D 88 LEU cc_start: 0.9431 (tp) cc_final: 0.9223 (tp) REVERT: D 90 LEU cc_start: 0.9329 (tp) cc_final: 0.8985 (tp) REVERT: D 636 ASP cc_start: 0.8400 (t70) cc_final: 0.8166 (t0) REVERT: F 57 HIS cc_start: 0.6071 (m90) cc_final: 0.5595 (m170) REVERT: F 240 MET cc_start: 0.7472 (tpt) cc_final: 0.6832 (tpt) REVERT: F 243 MET cc_start: 0.7425 (tpp) cc_final: 0.6848 (tpp) REVERT: F 258 TRP cc_start: 0.7859 (m100) cc_final: 0.7172 (m100) REVERT: F 286 CYS cc_start: 0.7481 (t) cc_final: 0.7130 (t) REVERT: G 57 HIS cc_start: 0.6079 (m90) cc_final: 0.5614 (m170) REVERT: G 240 MET cc_start: 0.7487 (tpt) cc_final: 0.6845 (tpt) REVERT: G 243 MET cc_start: 0.7441 (tpp) cc_final: 0.6866 (tpp) REVERT: G 258 TRP cc_start: 0.7863 (m100) cc_final: 0.7177 (m100) REVERT: G 286 CYS cc_start: 0.7491 (t) cc_final: 0.7130 (t) REVERT: H 57 HIS cc_start: 0.6084 (m90) cc_final: 0.5614 (m170) REVERT: H 240 MET cc_start: 0.7470 (tpt) cc_final: 0.6834 (tpt) REVERT: H 243 MET cc_start: 0.7426 (tpp) cc_final: 0.6852 (tpp) REVERT: H 258 TRP cc_start: 0.7883 (m100) cc_final: 0.7199 (m100) REVERT: H 286 CYS cc_start: 0.7488 (t) cc_final: 0.7134 (t) outliers start: 16 outliers final: 4 residues processed: 524 average time/residue: 0.2109 time to fit residues: 178.3043 Evaluate side-chains 360 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 356 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 56 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS G 244 HIS H 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.101747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.075571 restraints weight = 75501.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.074810 restraints weight = 64583.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075419 restraints weight = 55976.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.075816 restraints weight = 43380.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.075851 restraints weight = 40324.428| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33596 Z= 0.151 Angle : 0.563 8.851 45440 Z= 0.295 Chirality : 0.040 0.137 5080 Planarity : 0.004 0.037 5652 Dihedral : 12.885 145.325 4916 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.04 % Allowed : 7.05 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.13), residues: 3928 helix: 1.42 (0.10), residues: 2548 sheet: -1.07 (0.40), residues: 152 loop : -0.34 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 119 TYR 0.021 0.001 TYR D 118 PHE 0.017 0.002 PHE A 319 TRP 0.020 0.001 TRP D 327 HIS 0.005 0.001 HIS D 735 Details of bonding type rmsd covalent geometry : bond 0.00346 (33576) covalent geometry : angle 0.56165 (45420) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.56567 ( 8) hydrogen bonds : bond 0.04715 ( 1892) hydrogen bonds : angle 4.14517 ( 5448) metal coordination : bond 0.00477 ( 16) metal coordination : angle 2.22470 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 415 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7520 (tp30) cc_final: 0.7267 (tp30) REVERT: A 361 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8578 (mtpp) REVERT: A 422 MET cc_start: 0.7229 (ttm) cc_final: 0.7010 (ttt) REVERT: E 198 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.5286 (ptt) REVERT: E 214 CYS cc_start: 0.8033 (t) cc_final: 0.7608 (t) REVERT: E 243 MET cc_start: 0.8135 (tpp) cc_final: 0.7747 (tpp) REVERT: E 247 MET cc_start: 0.8133 (mmm) cc_final: 0.7691 (tmm) REVERT: E 258 TRP cc_start: 0.7916 (m100) cc_final: 0.7154 (m100) REVERT: E 310 LEU cc_start: 0.7958 (mt) cc_final: 0.7522 (mt) REVERT: B 87 GLU cc_start: 0.7511 (tp30) cc_final: 0.7259 (tp30) REVERT: B 361 LYS cc_start: 0.8813 (mtpp) cc_final: 0.8580 (mtpp) REVERT: B 422 MET cc_start: 0.7236 (ttm) cc_final: 0.7020 (ttt) REVERT: C 87 GLU cc_start: 0.7534 (tp30) cc_final: 0.7274 (tp30) REVERT: C 361 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8582 (mtpp) REVERT: C 422 MET cc_start: 0.7247 (ttm) cc_final: 0.7031 (ttt) REVERT: D 69 LEU cc_start: 0.7156 (tp) cc_final: 0.6872 (tt) REVERT: D 87 GLU cc_start: 0.7522 (tp30) cc_final: 0.7270 (tp30) REVERT: D 361 LYS cc_start: 0.8809 (mtpp) cc_final: 0.8578 (mtpp) REVERT: D 422 MET cc_start: 0.7245 (ttm) cc_final: 0.7029 (ttt) REVERT: F 214 CYS cc_start: 0.8020 (t) cc_final: 0.7610 (t) REVERT: F 243 MET cc_start: 0.8161 (tpp) cc_final: 0.7730 (tpp) REVERT: F 247 MET cc_start: 0.8124 (mmm) cc_final: 0.7692 (tmm) REVERT: F 258 TRP cc_start: 0.7904 (m100) cc_final: 0.7134 (m100) REVERT: F 310 LEU cc_start: 0.7975 (mt) cc_final: 0.7533 (mt) REVERT: G 214 CYS cc_start: 0.8027 (t) cc_final: 0.7611 (t) REVERT: G 243 MET cc_start: 0.8165 (tpp) cc_final: 0.7737 (tpp) REVERT: G 247 MET cc_start: 0.8141 (mmm) cc_final: 0.7695 (tmm) REVERT: G 258 TRP cc_start: 0.7921 (m100) cc_final: 0.7147 (m100) REVERT: G 310 LEU cc_start: 0.7968 (mt) cc_final: 0.7519 (mt) REVERT: H 214 CYS cc_start: 0.8017 (t) cc_final: 0.7605 (t) REVERT: H 243 MET cc_start: 0.8167 (tpp) cc_final: 0.7739 (tpp) REVERT: H 247 MET cc_start: 0.8138 (mmm) cc_final: 0.7696 (tmm) REVERT: H 258 TRP cc_start: 0.7934 (m100) cc_final: 0.7164 (m100) REVERT: H 310 LEU cc_start: 0.7969 (mt) cc_final: 0.7518 (mt) outliers start: 37 outliers final: 16 residues processed: 427 average time/residue: 0.2069 time to fit residues: 145.0435 Evaluate side-chains 367 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 350 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain H residue 187 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 164 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 323 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 354 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 443 ASN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS B 53 GLN B 443 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS ** G 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 HIS ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.072938 restraints weight = 74878.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.072714 restraints weight = 55144.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.073313 restraints weight = 44348.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.073828 restraints weight = 38228.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.073899 restraints weight = 35888.855| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33596 Z= 0.146 Angle : 0.515 7.538 45440 Z= 0.267 Chirality : 0.039 0.138 5080 Planarity : 0.003 0.034 5652 Dihedral : 11.763 152.401 4908 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.55 % Allowed : 8.74 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.14), residues: 3928 helix: 1.77 (0.10), residues: 2568 sheet: -1.38 (0.39), residues: 152 loop : -0.19 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 464 TYR 0.014 0.001 TYR C 524 PHE 0.020 0.001 PHE E 189 TRP 0.017 0.001 TRP A 327 HIS 0.008 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00334 (33576) covalent geometry : angle 0.51443 (45420) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.60290 ( 8) hydrogen bonds : bond 0.04466 ( 1892) hydrogen bonds : angle 3.91886 ( 5448) metal coordination : bond 0.00497 ( 16) metal coordination : angle 1.59819 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 375 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.7555 (mmm) cc_final: 0.7309 (tpt) REVERT: A 86 MET cc_start: 0.8179 (mtt) cc_final: 0.7969 (mtt) REVERT: A 87 GLU cc_start: 0.7525 (tp30) cc_final: 0.7063 (tp30) REVERT: A 90 LEU cc_start: 0.8978 (tp) cc_final: 0.8641 (tp) REVERT: A 212 SER cc_start: 0.8689 (m) cc_final: 0.8257 (p) REVERT: A 327 TRP cc_start: 0.8402 (p-90) cc_final: 0.8155 (p-90) REVERT: A 422 MET cc_start: 0.7287 (ttm) cc_final: 0.7045 (ttt) REVERT: E 214 CYS cc_start: 0.8018 (t) cc_final: 0.7546 (t) REVERT: E 243 MET cc_start: 0.8194 (tpp) cc_final: 0.7514 (tpp) REVERT: E 247 MET cc_start: 0.8162 (mmm) cc_final: 0.7686 (tmm) REVERT: E 258 TRP cc_start: 0.8069 (m100) cc_final: 0.7363 (m100) REVERT: E 310 LEU cc_start: 0.7952 (mt) cc_final: 0.7608 (mt) REVERT: E 336 PHE cc_start: 0.8187 (t80) cc_final: 0.7980 (t80) REVERT: B 66 MET cc_start: 0.7568 (mmm) cc_final: 0.7329 (tpt) REVERT: B 86 MET cc_start: 0.8168 (mtt) cc_final: 0.7963 (mtt) REVERT: B 87 GLU cc_start: 0.7520 (tp30) cc_final: 0.7067 (tp30) REVERT: B 90 LEU cc_start: 0.8976 (tp) cc_final: 0.8634 (tp) REVERT: B 212 SER cc_start: 0.8686 (m) cc_final: 0.8253 (p) REVERT: B 327 TRP cc_start: 0.8400 (p-90) cc_final: 0.8166 (p-90) REVERT: B 422 MET cc_start: 0.7293 (ttm) cc_final: 0.7050 (ttt) REVERT: C 66 MET cc_start: 0.7568 (mmm) cc_final: 0.7325 (tpt) REVERT: C 86 MET cc_start: 0.8180 (mtt) cc_final: 0.7969 (mtt) REVERT: C 87 GLU cc_start: 0.7520 (tp30) cc_final: 0.7066 (tp30) REVERT: C 90 LEU cc_start: 0.8976 (tp) cc_final: 0.8634 (tp) REVERT: C 212 SER cc_start: 0.8683 (m) cc_final: 0.8252 (p) REVERT: C 327 TRP cc_start: 0.8400 (p-90) cc_final: 0.8165 (p-90) REVERT: C 422 MET cc_start: 0.7295 (ttm) cc_final: 0.7058 (ttt) REVERT: D 66 MET cc_start: 0.7548 (mmm) cc_final: 0.7302 (tpt) REVERT: D 86 MET cc_start: 0.8178 (mtt) cc_final: 0.7968 (mtt) REVERT: D 87 GLU cc_start: 0.7539 (tp30) cc_final: 0.7084 (tp30) REVERT: D 90 LEU cc_start: 0.8978 (tp) cc_final: 0.8643 (tp) REVERT: D 212 SER cc_start: 0.8690 (m) cc_final: 0.8257 (p) REVERT: D 327 TRP cc_start: 0.8397 (p-90) cc_final: 0.8159 (p-90) REVERT: D 422 MET cc_start: 0.7284 (ttm) cc_final: 0.7053 (ttt) REVERT: F 214 CYS cc_start: 0.7972 (t) cc_final: 0.7537 (t) REVERT: F 243 MET cc_start: 0.8182 (tpp) cc_final: 0.7502 (tpp) REVERT: F 247 MET cc_start: 0.8160 (mmm) cc_final: 0.7687 (tmm) REVERT: F 258 TRP cc_start: 0.8078 (m100) cc_final: 0.7434 (m100) REVERT: F 310 LEU cc_start: 0.7959 (mt) cc_final: 0.7624 (mt) REVERT: G 214 CYS cc_start: 0.7973 (t) cc_final: 0.7533 (t) REVERT: G 243 MET cc_start: 0.8198 (tpp) cc_final: 0.7522 (tpp) REVERT: G 247 MET cc_start: 0.8171 (mmm) cc_final: 0.7689 (tmm) REVERT: G 258 TRP cc_start: 0.8092 (m100) cc_final: 0.7408 (m100) REVERT: G 310 LEU cc_start: 0.7958 (mt) cc_final: 0.7624 (mt) REVERT: H 214 CYS cc_start: 0.7950 (t) cc_final: 0.7511 (t) REVERT: H 243 MET cc_start: 0.8194 (tpp) cc_final: 0.7512 (tpp) REVERT: H 247 MET cc_start: 0.8169 (mmm) cc_final: 0.7686 (tmm) REVERT: H 258 TRP cc_start: 0.8097 (m100) cc_final: 0.7422 (m100) REVERT: H 310 LEU cc_start: 0.7962 (mt) cc_final: 0.7624 (mt) outliers start: 55 outliers final: 38 residues processed: 394 average time/residue: 0.2055 time to fit residues: 131.9769 Evaluate side-chains 378 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 254 CYS Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 254 CYS Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 254 CYS Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain H residue 187 THR Chi-restraints excluded: chain H residue 254 CYS Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 328 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 244 optimal weight: 0.0000 chunk 190 optimal weight: 0.2980 chunk 66 optimal weight: 9.9990 chunk 228 optimal weight: 0.0570 chunk 340 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 305 optimal weight: 20.0000 overall best weight: 1.2706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS ** G 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 HIS ** H 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.072990 restraints weight = 75056.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.071551 restraints weight = 62715.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.072148 restraints weight = 52895.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.072318 restraints weight = 44196.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.072509 restraints weight = 41438.904| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33596 Z= 0.141 Angle : 0.506 7.781 45440 Z= 0.262 Chirality : 0.039 0.134 5080 Planarity : 0.003 0.038 5652 Dihedral : 11.459 179.336 4908 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.30 % Allowed : 10.51 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.14), residues: 3928 helix: 1.92 (0.10), residues: 2572 sheet: -1.38 (0.38), residues: 172 loop : -0.12 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 324 TYR 0.014 0.001 TYR B 524 PHE 0.021 0.001 PHE D 319 TRP 0.015 0.001 TRP D 327 HIS 0.010 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00318 (33576) covalent geometry : angle 0.50493 (45420) SS BOND : bond 0.00233 ( 4) SS BOND : angle 0.61302 ( 8) hydrogen bonds : bond 0.04236 ( 1892) hydrogen bonds : angle 3.78840 ( 5448) metal coordination : bond 0.00488 ( 16) metal coordination : angle 1.56210 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 361 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7560 (tp30) cc_final: 0.6992 (tp30) REVERT: A 212 SER cc_start: 0.8653 (m) cc_final: 0.8219 (p) REVERT: A 327 TRP cc_start: 0.8382 (p-90) cc_final: 0.7954 (p-90) REVERT: A 422 MET cc_start: 0.7397 (ttm) cc_final: 0.7133 (ttt) REVERT: E 243 MET cc_start: 0.8220 (tpp) cc_final: 0.7587 (tpp) REVERT: E 247 MET cc_start: 0.8215 (mmm) cc_final: 0.7689 (tmm) REVERT: E 258 TRP cc_start: 0.8205 (m100) cc_final: 0.7750 (m100) REVERT: E 310 LEU cc_start: 0.8057 (mt) cc_final: 0.7742 (mt) REVERT: B 87 GLU cc_start: 0.7577 (tp30) cc_final: 0.6997 (tp30) REVERT: B 212 SER cc_start: 0.8652 (m) cc_final: 0.8218 (p) REVERT: B 327 TRP cc_start: 0.8386 (p-90) cc_final: 0.7962 (p-90) REVERT: B 422 MET cc_start: 0.7395 (ttm) cc_final: 0.7135 (ttt) REVERT: C 66 MET cc_start: 0.7631 (mmm) cc_final: 0.7392 (tpt) REVERT: C 87 GLU cc_start: 0.7559 (tp30) cc_final: 0.6989 (tp30) REVERT: C 212 SER cc_start: 0.8649 (m) cc_final: 0.8215 (p) REVERT: C 327 TRP cc_start: 0.8386 (p-90) cc_final: 0.7953 (p-90) REVERT: C 422 MET cc_start: 0.7391 (ttm) cc_final: 0.7137 (ttt) REVERT: D 87 GLU cc_start: 0.7582 (tp30) cc_final: 0.7007 (tp30) REVERT: D 212 SER cc_start: 0.8652 (m) cc_final: 0.8219 (p) REVERT: D 327 TRP cc_start: 0.8388 (p-90) cc_final: 0.7959 (p-90) REVERT: D 422 MET cc_start: 0.7375 (ttm) cc_final: 0.7128 (ttt) REVERT: F 37 LEU cc_start: 0.8799 (mt) cc_final: 0.8555 (mm) REVERT: F 53 MET cc_start: 0.8370 (ptp) cc_final: 0.7982 (ptp) REVERT: F 214 CYS cc_start: 0.7975 (t) cc_final: 0.7515 (t) REVERT: F 243 MET cc_start: 0.8268 (tpp) cc_final: 0.7610 (tpp) REVERT: F 247 MET cc_start: 0.8202 (mmm) cc_final: 0.7700 (tmm) REVERT: F 258 TRP cc_start: 0.8211 (m100) cc_final: 0.7472 (m100) REVERT: F 310 LEU cc_start: 0.8072 (mt) cc_final: 0.7757 (mt) REVERT: G 37 LEU cc_start: 0.8803 (mt) cc_final: 0.8559 (mm) REVERT: G 53 MET cc_start: 0.8343 (ptp) cc_final: 0.7978 (ptp) REVERT: G 214 CYS cc_start: 0.7985 (t) cc_final: 0.7530 (t) REVERT: G 243 MET cc_start: 0.8269 (tpp) cc_final: 0.7614 (tpp) REVERT: G 247 MET cc_start: 0.8213 (mmm) cc_final: 0.7694 (tmm) REVERT: G 258 TRP cc_start: 0.8228 (m100) cc_final: 0.7488 (m100) REVERT: G 310 LEU cc_start: 0.8071 (mt) cc_final: 0.7746 (mt) REVERT: H 37 LEU cc_start: 0.8812 (mt) cc_final: 0.8572 (mm) REVERT: H 53 MET cc_start: 0.8374 (ptp) cc_final: 0.7980 (ptp) REVERT: H 214 CYS cc_start: 0.7961 (t) cc_final: 0.7488 (t) REVERT: H 243 MET cc_start: 0.8284 (tpp) cc_final: 0.7620 (tpp) REVERT: H 247 MET cc_start: 0.8215 (mmm) cc_final: 0.7709 (tmm) REVERT: H 258 TRP cc_start: 0.8232 (m100) cc_final: 0.7687 (m100) REVERT: H 310 LEU cc_start: 0.8076 (mt) cc_final: 0.7757 (mt) outliers start: 46 outliers final: 33 residues processed: 377 average time/residue: 0.1956 time to fit residues: 123.9438 Evaluate side-chains 376 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 343 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 517 ILE Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 517 ILE Chi-restraints excluded: chain D residue 540 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 292 optimal weight: 0.0060 chunk 259 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 212 optimal weight: 0.0050 chunk 85 optimal weight: 0.8980 chunk 356 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 269 optimal weight: 0.9990 overall best weight: 0.9814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS G 244 HIS H 244 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.099309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.073259 restraints weight = 75365.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.071992 restraints weight = 61864.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.072741 restraints weight = 51201.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.072933 restraints weight = 42331.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.073072 restraints weight = 39633.516| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33596 Z= 0.119 Angle : 0.490 8.382 45440 Z= 0.248 Chirality : 0.038 0.157 5080 Planarity : 0.003 0.032 5652 Dihedral : 10.277 140.045 4908 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.55 % Allowed : 11.95 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.14), residues: 3928 helix: 2.05 (0.10), residues: 2568 sheet: -1.07 (0.39), residues: 172 loop : -0.09 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 178 TYR 0.015 0.001 TYR A 524 PHE 0.024 0.001 PHE E 189 TRP 0.014 0.001 TRP A 327 HIS 0.010 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00266 (33576) covalent geometry : angle 0.48942 (45420) SS BOND : bond 0.00224 ( 4) SS BOND : angle 0.52946 ( 8) hydrogen bonds : bond 0.04019 ( 1892) hydrogen bonds : angle 3.64517 ( 5448) metal coordination : bond 0.00407 ( 16) metal coordination : angle 1.33090 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 351 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7482 (tp30) cc_final: 0.7168 (tp30) REVERT: A 212 SER cc_start: 0.8623 (m) cc_final: 0.8219 (p) REVERT: A 422 MET cc_start: 0.7360 (ttm) cc_final: 0.7093 (ttt) REVERT: E 195 TYR cc_start: 0.6238 (OUTLIER) cc_final: 0.4101 (m-10) REVERT: E 243 MET cc_start: 0.8264 (tpp) cc_final: 0.7602 (tpp) REVERT: E 247 MET cc_start: 0.8227 (mmm) cc_final: 0.7701 (tmm) REVERT: E 258 TRP cc_start: 0.8280 (m100) cc_final: 0.7749 (m100) REVERT: E 310 LEU cc_start: 0.8033 (mt) cc_final: 0.7697 (mt) REVERT: B 66 MET cc_start: 0.7670 (mmm) cc_final: 0.7429 (tpt) REVERT: B 87 GLU cc_start: 0.7487 (tp30) cc_final: 0.7171 (tp30) REVERT: B 212 SER cc_start: 0.8631 (m) cc_final: 0.8223 (p) REVERT: B 422 MET cc_start: 0.7353 (ttm) cc_final: 0.7097 (ttt) REVERT: C 66 MET cc_start: 0.7683 (mmm) cc_final: 0.7437 (tpt) REVERT: C 87 GLU cc_start: 0.7489 (tp30) cc_final: 0.7165 (tp30) REVERT: C 212 SER cc_start: 0.8622 (m) cc_final: 0.8217 (p) REVERT: C 422 MET cc_start: 0.7361 (ttm) cc_final: 0.7095 (ttt) REVERT: D 66 MET cc_start: 0.7685 (mmm) cc_final: 0.7450 (tpt) REVERT: D 87 GLU cc_start: 0.7498 (tp30) cc_final: 0.7174 (tp30) REVERT: D 212 SER cc_start: 0.8622 (m) cc_final: 0.8217 (p) REVERT: D 422 MET cc_start: 0.7342 (ttm) cc_final: 0.7093 (ttt) REVERT: F 53 MET cc_start: 0.8287 (ptp) cc_final: 0.7927 (ptp) REVERT: F 243 MET cc_start: 0.8246 (tpp) cc_final: 0.7598 (tpp) REVERT: F 247 MET cc_start: 0.8222 (mmm) cc_final: 0.7705 (tmm) REVERT: F 258 TRP cc_start: 0.8272 (m100) cc_final: 0.7715 (m100) REVERT: F 310 LEU cc_start: 0.8069 (mt) cc_final: 0.7738 (mt) REVERT: G 37 LEU cc_start: 0.8760 (mt) cc_final: 0.8538 (mm) REVERT: G 53 MET cc_start: 0.8270 (ptp) cc_final: 0.7987 (ptp) REVERT: G 214 CYS cc_start: 0.7941 (t) cc_final: 0.7504 (t) REVERT: G 243 MET cc_start: 0.8248 (tpp) cc_final: 0.7604 (tpp) REVERT: G 247 MET cc_start: 0.8217 (mmm) cc_final: 0.7695 (tmm) REVERT: G 258 TRP cc_start: 0.8293 (m100) cc_final: 0.7682 (m100) REVERT: G 310 LEU cc_start: 0.8078 (mt) cc_final: 0.7744 (mt) REVERT: H 37 LEU cc_start: 0.8759 (mt) cc_final: 0.8531 (mm) REVERT: H 53 MET cc_start: 0.8293 (ptp) cc_final: 0.7933 (ptp) REVERT: H 214 CYS cc_start: 0.7941 (t) cc_final: 0.7500 (t) REVERT: H 243 MET cc_start: 0.8270 (tpp) cc_final: 0.7611 (tpp) REVERT: H 247 MET cc_start: 0.8230 (mmm) cc_final: 0.7716 (tmm) REVERT: H 258 TRP cc_start: 0.8288 (m100) cc_final: 0.7699 (m100) REVERT: H 310 LEU cc_start: 0.8041 (mt) cc_final: 0.7698 (mt) outliers start: 55 outliers final: 36 residues processed: 376 average time/residue: 0.2115 time to fit residues: 133.0648 Evaluate side-chains 380 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 460 TYR Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 206 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN E 244 HIS E 306 GLN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 ASN C 53 GLN ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 ASN D 60 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS F 306 GLN G 244 HIS G 306 GLN H 244 HIS H 306 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.094951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.068919 restraints weight = 75658.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.068418 restraints weight = 69010.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.068932 restraints weight = 59836.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.069168 restraints weight = 48829.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.069237 restraints weight = 45911.108| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 33596 Z= 0.321 Angle : 0.696 9.954 45440 Z= 0.350 Chirality : 0.044 0.170 5080 Planarity : 0.004 0.034 5652 Dihedral : 11.117 149.959 4908 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.03 % Allowed : 13.11 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.14), residues: 3928 helix: 1.82 (0.10), residues: 2540 sheet: -0.77 (0.39), residues: 160 loop : -0.15 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 643 TYR 0.021 0.002 TYR B 524 PHE 0.019 0.002 PHE A 531 TRP 0.020 0.002 TRP A 315 HIS 0.010 0.002 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00758 (33576) covalent geometry : angle 0.69583 (45420) SS BOND : bond 0.00516 ( 4) SS BOND : angle 1.09025 ( 8) hydrogen bonds : bond 0.05501 ( 1892) hydrogen bonds : angle 4.02350 ( 5448) metal coordination : bond 0.00688 ( 16) metal coordination : angle 1.22267 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 338 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7413 (tp30) cc_final: 0.7145 (tp30) REVERT: A 212 SER cc_start: 0.8763 (m) cc_final: 0.8465 (p) REVERT: A 422 MET cc_start: 0.7429 (ttm) cc_final: 0.7190 (ttt) REVERT: A 624 MET cc_start: 0.7962 (mtm) cc_final: 0.7742 (mtm) REVERT: A 636 ASP cc_start: 0.8365 (t70) cc_final: 0.8124 (t0) REVERT: E 195 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.3660 (m-10) REVERT: E 243 MET cc_start: 0.8218 (tpp) cc_final: 0.7634 (tpp) REVERT: E 247 MET cc_start: 0.8322 (mmm) cc_final: 0.7703 (tmm) REVERT: E 258 TRP cc_start: 0.8571 (m100) cc_final: 0.8006 (m100) REVERT: E 310 LEU cc_start: 0.8276 (mt) cc_final: 0.7997 (mt) REVERT: B 87 GLU cc_start: 0.7434 (tp30) cc_final: 0.7152 (tp30) REVERT: B 212 SER cc_start: 0.8758 (m) cc_final: 0.8468 (p) REVERT: B 422 MET cc_start: 0.7421 (ttm) cc_final: 0.7188 (ttt) REVERT: B 636 ASP cc_start: 0.8335 (t70) cc_final: 0.8117 (t0) REVERT: C 87 GLU cc_start: 0.7425 (tp30) cc_final: 0.7145 (tp30) REVERT: C 212 SER cc_start: 0.8763 (m) cc_final: 0.8470 (p) REVERT: C 422 MET cc_start: 0.7413 (ttm) cc_final: 0.7179 (ttt) REVERT: C 636 ASP cc_start: 0.8355 (t70) cc_final: 0.8127 (t0) REVERT: D 87 GLU cc_start: 0.7434 (tp30) cc_final: 0.7174 (tp30) REVERT: D 212 SER cc_start: 0.8760 (m) cc_final: 0.8465 (p) REVERT: D 422 MET cc_start: 0.7423 (ttm) cc_final: 0.7192 (ttt) REVERT: D 636 ASP cc_start: 0.8345 (t70) cc_final: 0.8120 (t0) REVERT: F 53 MET cc_start: 0.8190 (ptp) cc_final: 0.7861 (ptp) REVERT: F 195 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.3426 (m-10) REVERT: F 243 MET cc_start: 0.8234 (tpp) cc_final: 0.7615 (tpp) REVERT: F 247 MET cc_start: 0.8313 (mmm) cc_final: 0.7715 (tmm) REVERT: F 258 TRP cc_start: 0.8543 (m100) cc_final: 0.7990 (m100) REVERT: F 310 LEU cc_start: 0.8274 (mt) cc_final: 0.8004 (mt) REVERT: G 53 MET cc_start: 0.8183 (ptp) cc_final: 0.7926 (ptp) REVERT: G 195 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.3405 (m-10) REVERT: G 243 MET cc_start: 0.8249 (tpp) cc_final: 0.7636 (tpp) REVERT: G 247 MET cc_start: 0.8321 (mmm) cc_final: 0.7697 (tmm) REVERT: G 258 TRP cc_start: 0.8537 (m100) cc_final: 0.7984 (m100) REVERT: H 53 MET cc_start: 0.8197 (ptp) cc_final: 0.7869 (ptp) REVERT: H 195 TYR cc_start: 0.6248 (OUTLIER) cc_final: 0.3399 (m-10) REVERT: H 243 MET cc_start: 0.8239 (tpp) cc_final: 0.7615 (tpp) REVERT: H 247 MET cc_start: 0.8324 (mmm) cc_final: 0.7706 (tmm) REVERT: H 258 TRP cc_start: 0.8558 (m100) cc_final: 0.8023 (m100) REVERT: H 310 LEU cc_start: 0.8271 (mt) cc_final: 0.8068 (mt) outliers start: 72 outliers final: 47 residues processed: 370 average time/residue: 0.2028 time to fit residues: 126.4343 Evaluate side-chains 387 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 336 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 460 TYR Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 517 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain H residue 195 TYR Chi-restraints excluded: chain H residue 305 CYS Chi-restraints excluded: chain H residue 339 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 290 optimal weight: 0.0770 chunk 148 optimal weight: 0.8980 chunk 288 optimal weight: 0.8980 chunk 354 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 383 optimal weight: 4.9990 chunk 367 optimal weight: 20.0000 chunk 297 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS B 60 ASN B 396 GLN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS G 244 HIS H 244 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.071998 restraints weight = 75171.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.070619 restraints weight = 58355.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.071309 restraints weight = 49698.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.071490 restraints weight = 41619.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.071641 restraints weight = 39530.638| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33596 Z= 0.113 Angle : 0.505 7.834 45440 Z= 0.256 Chirality : 0.038 0.207 5080 Planarity : 0.003 0.032 5652 Dihedral : 10.423 140.023 4908 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.10 % Allowed : 14.40 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.14), residues: 3928 helix: 2.01 (0.10), residues: 2576 sheet: -0.61 (0.39), residues: 160 loop : -0.13 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 120 TYR 0.016 0.001 TYR A 524 PHE 0.015 0.001 PHE E 189 TRP 0.013 0.001 TRP A 315 HIS 0.005 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00245 (33576) covalent geometry : angle 0.50506 (45420) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.63697 ( 8) hydrogen bonds : bond 0.04208 ( 1892) hydrogen bonds : angle 3.64843 ( 5448) metal coordination : bond 0.00492 ( 16) metal coordination : angle 1.19215 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 335 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7318 (tp30) cc_final: 0.6669 (tp30) REVERT: A 212 SER cc_start: 0.8708 (m) cc_final: 0.8353 (p) REVERT: A 422 MET cc_start: 0.7380 (ttm) cc_final: 0.7177 (ttt) REVERT: E 195 TYR cc_start: 0.6251 (OUTLIER) cc_final: 0.3590 (m-10) REVERT: E 243 MET cc_start: 0.8238 (tpp) cc_final: 0.7556 (tpp) REVERT: E 247 MET cc_start: 0.8284 (mmm) cc_final: 0.7616 (tmm) REVERT: E 258 TRP cc_start: 0.8552 (m100) cc_final: 0.7885 (m100) REVERT: E 310 LEU cc_start: 0.8165 (mt) cc_final: 0.7827 (mt) REVERT: B 87 GLU cc_start: 0.7327 (tp30) cc_final: 0.6672 (tp30) REVERT: B 212 SER cc_start: 0.8703 (m) cc_final: 0.8351 (p) REVERT: B 422 MET cc_start: 0.7373 (ttm) cc_final: 0.7161 (ttt) REVERT: C 87 GLU cc_start: 0.7331 (tp30) cc_final: 0.6679 (tp30) REVERT: C 212 SER cc_start: 0.8713 (m) cc_final: 0.8352 (p) REVERT: C 422 MET cc_start: 0.7383 (ttm) cc_final: 0.7169 (ttt) REVERT: D 87 GLU cc_start: 0.7345 (tp30) cc_final: 0.6687 (tp30) REVERT: D 212 SER cc_start: 0.8715 (m) cc_final: 0.8352 (p) REVERT: D 422 MET cc_start: 0.7390 (ttm) cc_final: 0.7174 (ttt) REVERT: F 53 MET cc_start: 0.8357 (ptp) cc_final: 0.7963 (ptp) REVERT: F 243 MET cc_start: 0.8211 (tpp) cc_final: 0.7539 (tpp) REVERT: F 247 MET cc_start: 0.8278 (mmm) cc_final: 0.7631 (tmm) REVERT: F 258 TRP cc_start: 0.8527 (m100) cc_final: 0.7849 (m100) REVERT: F 310 LEU cc_start: 0.8163 (mt) cc_final: 0.7827 (mt) REVERT: G 53 MET cc_start: 0.8286 (ptp) cc_final: 0.8024 (ptp) REVERT: G 243 MET cc_start: 0.8257 (tpp) cc_final: 0.7548 (tpp) REVERT: G 247 MET cc_start: 0.8338 (mmm) cc_final: 0.7737 (tmm) REVERT: G 258 TRP cc_start: 0.8508 (m100) cc_final: 0.7887 (m100) REVERT: H 53 MET cc_start: 0.8297 (ptp) cc_final: 0.7956 (ptp) REVERT: H 243 MET cc_start: 0.8256 (tpp) cc_final: 0.7542 (tpp) REVERT: H 247 MET cc_start: 0.8288 (mmm) cc_final: 0.7634 (tmm) REVERT: H 258 TRP cc_start: 0.8563 (m100) cc_final: 0.7892 (m100) REVERT: H 310 LEU cc_start: 0.8164 (mt) cc_final: 0.7825 (mt) outliers start: 39 outliers final: 28 residues processed: 351 average time/residue: 0.2031 time to fit residues: 119.2895 Evaluate side-chains 353 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 324 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 460 TYR Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 507 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 256 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 313 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 54 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 250 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 GLN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.073007 restraints weight = 75699.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.071648 restraints weight = 59429.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.072190 restraints weight = 50973.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.073315 restraints weight = 42191.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073286 restraints weight = 36631.138| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33596 Z= 0.104 Angle : 0.487 8.307 45440 Z= 0.246 Chirality : 0.037 0.126 5080 Planarity : 0.003 0.031 5652 Dihedral : 10.034 141.779 4908 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.27 % Allowed : 14.26 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.14), residues: 3928 helix: 2.18 (0.10), residues: 2552 sheet: -0.48 (0.41), residues: 160 loop : 0.12 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 178 TYR 0.014 0.001 TYR B 524 PHE 0.014 0.001 PHE E 189 TRP 0.033 0.001 TRP G 211 HIS 0.007 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00222 (33576) covalent geometry : angle 0.48646 (45420) SS BOND : bond 0.00250 ( 4) SS BOND : angle 0.48426 ( 8) hydrogen bonds : bond 0.03778 ( 1892) hydrogen bonds : angle 3.52037 ( 5448) metal coordination : bond 0.00411 ( 16) metal coordination : angle 1.24905 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 364 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7292 (tp30) cc_final: 0.6629 (tp30) REVERT: A 212 SER cc_start: 0.8648 (m) cc_final: 0.8281 (p) REVERT: A 422 MET cc_start: 0.7369 (ttm) cc_final: 0.7132 (ttt) REVERT: A 619 MET cc_start: 0.7691 (ttm) cc_final: 0.7466 (ttm) REVERT: E 195 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.3824 (m-10) REVERT: E 243 MET cc_start: 0.8238 (tpp) cc_final: 0.7568 (tpp) REVERT: E 247 MET cc_start: 0.8209 (mmm) cc_final: 0.7589 (tmm) REVERT: E 258 TRP cc_start: 0.8600 (m100) cc_final: 0.7812 (m100) REVERT: E 310 LEU cc_start: 0.8131 (mt) cc_final: 0.7776 (mt) REVERT: B 87 GLU cc_start: 0.7288 (tp30) cc_final: 0.6630 (tp30) REVERT: B 212 SER cc_start: 0.8647 (m) cc_final: 0.8282 (p) REVERT: B 422 MET cc_start: 0.7377 (ttm) cc_final: 0.7145 (ttt) REVERT: C 66 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7371 (tmm) REVERT: C 87 GLU cc_start: 0.7301 (tp30) cc_final: 0.6644 (tp30) REVERT: C 212 SER cc_start: 0.8646 (m) cc_final: 0.8281 (p) REVERT: C 422 MET cc_start: 0.7375 (ttm) cc_final: 0.7139 (ttt) REVERT: D 87 GLU cc_start: 0.7278 (tp30) cc_final: 0.6611 (tp30) REVERT: D 212 SER cc_start: 0.8649 (m) cc_final: 0.8275 (p) REVERT: D 422 MET cc_start: 0.7381 (ttm) cc_final: 0.7154 (ttt) REVERT: F 53 MET cc_start: 0.8337 (ptp) cc_final: 0.8000 (ptp) REVERT: F 195 TYR cc_start: 0.6372 (OUTLIER) cc_final: 0.3529 (m-10) REVERT: F 243 MET cc_start: 0.8248 (tpp) cc_final: 0.7553 (tpp) REVERT: F 247 MET cc_start: 0.8199 (mmm) cc_final: 0.7598 (tmm) REVERT: F 258 TRP cc_start: 0.8586 (m100) cc_final: 0.7816 (m100) REVERT: F 310 LEU cc_start: 0.8122 (mt) cc_final: 0.7771 (mt) REVERT: G 53 MET cc_start: 0.8333 (ptp) cc_final: 0.8006 (ptp) REVERT: G 195 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.3603 (m-10) REVERT: G 243 MET cc_start: 0.8263 (tpp) cc_final: 0.7540 (tpp) REVERT: G 247 MET cc_start: 0.8310 (mmm) cc_final: 0.7793 (tmm) REVERT: G 258 TRP cc_start: 0.8555 (m100) cc_final: 0.7877 (m100) REVERT: H 53 MET cc_start: 0.8357 (ptp) cc_final: 0.8023 (ptp) REVERT: H 195 TYR cc_start: 0.6382 (OUTLIER) cc_final: 0.3540 (m-10) REVERT: H 243 MET cc_start: 0.8258 (tpp) cc_final: 0.7551 (tpp) REVERT: H 247 MET cc_start: 0.8169 (mmm) cc_final: 0.7563 (tmm) REVERT: H 258 TRP cc_start: 0.8575 (m100) cc_final: 0.7779 (m100) REVERT: H 310 LEU cc_start: 0.8122 (mt) cc_final: 0.7771 (mt) outliers start: 45 outliers final: 31 residues processed: 387 average time/residue: 0.2090 time to fit residues: 134.2168 Evaluate side-chains 375 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 339 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 460 TYR Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain H residue 195 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 131 optimal weight: 0.5980 chunk 180 optimal weight: 0.4980 chunk 299 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 387 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS B 154 ASN ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS ** G 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 HIS H 244 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.073063 restraints weight = 75166.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.073205 restraints weight = 69727.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073725 restraints weight = 56419.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.073921 restraints weight = 43559.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.073946 restraints weight = 41724.889| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33596 Z= 0.107 Angle : 0.501 8.863 45440 Z= 0.252 Chirality : 0.037 0.137 5080 Planarity : 0.003 0.031 5652 Dihedral : 9.931 143.771 4908 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.16 % Allowed : 14.88 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.14), residues: 3928 helix: 2.20 (0.10), residues: 2560 sheet: -0.44 (0.41), residues: 160 loop : 0.10 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 144 TYR 0.014 0.001 TYR A 524 PHE 0.014 0.001 PHE B 341 TRP 0.052 0.001 TRP G 211 HIS 0.005 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00234 (33576) covalent geometry : angle 0.50104 (45420) SS BOND : bond 0.00205 ( 4) SS BOND : angle 0.44078 ( 8) hydrogen bonds : bond 0.03723 ( 1892) hydrogen bonds : angle 3.47951 ( 5448) metal coordination : bond 0.00340 ( 16) metal coordination : angle 1.12706 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 355 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7160 (tp30) cc_final: 0.6537 (tp30) REVERT: A 212 SER cc_start: 0.8657 (m) cc_final: 0.8287 (p) REVERT: A 422 MET cc_start: 0.7367 (ttm) cc_final: 0.7144 (ttt) REVERT: E 139 CYS cc_start: 0.7499 (t) cc_final: 0.7148 (t) REVERT: E 195 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.3733 (m-10) REVERT: E 243 MET cc_start: 0.8141 (tpp) cc_final: 0.7515 (tpp) REVERT: E 247 MET cc_start: 0.8053 (mmm) cc_final: 0.7489 (tmm) REVERT: E 258 TRP cc_start: 0.8571 (m100) cc_final: 0.7884 (m100) REVERT: E 310 LEU cc_start: 0.8052 (mt) cc_final: 0.7680 (mt) REVERT: B 87 GLU cc_start: 0.7157 (tp30) cc_final: 0.6521 (tp30) REVERT: B 212 SER cc_start: 0.8660 (m) cc_final: 0.8287 (p) REVERT: B 422 MET cc_start: 0.7368 (ttm) cc_final: 0.7147 (ttt) REVERT: B 516 ASP cc_start: 0.6826 (m-30) cc_final: 0.6499 (m-30) REVERT: B 624 MET cc_start: 0.8096 (ptp) cc_final: 0.7764 (mtm) REVERT: C 66 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7319 (tmm) REVERT: C 87 GLU cc_start: 0.7181 (tp30) cc_final: 0.6542 (tp30) REVERT: C 212 SER cc_start: 0.8658 (m) cc_final: 0.8291 (p) REVERT: C 422 MET cc_start: 0.7373 (ttm) cc_final: 0.7140 (ttt) REVERT: C 516 ASP cc_start: 0.6816 (m-30) cc_final: 0.6485 (m-30) REVERT: C 624 MET cc_start: 0.8122 (ptp) cc_final: 0.7790 (mtm) REVERT: D 87 GLU cc_start: 0.7157 (tp30) cc_final: 0.6532 (tp30) REVERT: D 130 LEU cc_start: 0.8209 (tp) cc_final: 0.7967 (tt) REVERT: D 212 SER cc_start: 0.8657 (m) cc_final: 0.8281 (p) REVERT: D 422 MET cc_start: 0.7382 (ttm) cc_final: 0.7147 (ttt) REVERT: D 516 ASP cc_start: 0.6772 (m-30) cc_final: 0.6457 (m-30) REVERT: D 624 MET cc_start: 0.8130 (ptp) cc_final: 0.7577 (mtm) REVERT: F 53 MET cc_start: 0.8198 (ptp) cc_final: 0.7918 (ptp) REVERT: F 195 TYR cc_start: 0.6304 (OUTLIER) cc_final: 0.3521 (m-10) REVERT: F 243 MET cc_start: 0.8131 (tpp) cc_final: 0.7495 (tpp) REVERT: F 247 MET cc_start: 0.8053 (mmm) cc_final: 0.7509 (tmm) REVERT: F 258 TRP cc_start: 0.8538 (m100) cc_final: 0.7808 (m100) REVERT: F 310 LEU cc_start: 0.8048 (mt) cc_final: 0.7683 (mt) REVERT: G 53 MET cc_start: 0.8197 (ptp) cc_final: 0.7953 (ptp) REVERT: G 139 CYS cc_start: 0.7511 (t) cc_final: 0.7163 (t) REVERT: G 195 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.3380 (m-10) REVERT: G 243 MET cc_start: 0.8101 (tpp) cc_final: 0.7475 (tpp) REVERT: G 247 MET cc_start: 0.8200 (mmm) cc_final: 0.7782 (tmm) REVERT: G 258 TRP cc_start: 0.8547 (m100) cc_final: 0.7809 (m100) REVERT: H 53 MET cc_start: 0.8213 (ptp) cc_final: 0.7931 (ptp) REVERT: H 139 CYS cc_start: 0.7496 (t) cc_final: 0.7150 (t) REVERT: H 195 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.3504 (m-10) REVERT: H 243 MET cc_start: 0.8099 (tpp) cc_final: 0.7464 (tpp) REVERT: H 247 MET cc_start: 0.8063 (mmm) cc_final: 0.7524 (tmm) REVERT: H 258 TRP cc_start: 0.8554 (m100) cc_final: 0.7813 (m100) REVERT: H 310 LEU cc_start: 0.8051 (mt) cc_final: 0.7681 (mt) outliers start: 41 outliers final: 33 residues processed: 379 average time/residue: 0.2028 time to fit residues: 128.5244 Evaluate side-chains 380 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 342 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 460 TYR Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain H residue 195 TYR Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 79 optimal weight: 7.9990 chunk 386 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 chunk 286 optimal weight: 0.1980 chunk 231 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 361 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS ** G 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.098333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.072111 restraints weight = 75870.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.072188 restraints weight = 68121.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072710 restraints weight = 55736.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.072939 restraints weight = 42711.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.072976 restraints weight = 40619.943| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33596 Z= 0.134 Angle : 0.527 8.864 45440 Z= 0.265 Chirality : 0.038 0.132 5080 Planarity : 0.003 0.031 5652 Dihedral : 9.964 145.449 4908 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.21 % Allowed : 15.11 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.14), residues: 3928 helix: 2.21 (0.10), residues: 2560 sheet: -0.40 (0.41), residues: 160 loop : 0.14 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 144 TYR 0.016 0.001 TYR A 524 PHE 0.032 0.001 PHE E 336 TRP 0.065 0.001 TRP E 211 HIS 0.006 0.001 HIS E 244 Details of bonding type rmsd covalent geometry : bond 0.00309 (33576) covalent geometry : angle 0.52684 (45420) SS BOND : bond 0.00246 ( 4) SS BOND : angle 0.52300 ( 8) hydrogen bonds : bond 0.03909 ( 1892) hydrogen bonds : angle 3.49878 ( 5448) metal coordination : bond 0.00365 ( 16) metal coordination : angle 1.10537 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7856 Ramachandran restraints generated. 3928 Oldfield, 0 Emsley, 3928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 346 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7207 (tp30) cc_final: 0.6602 (tp30) REVERT: A 212 SER cc_start: 0.8702 (m) cc_final: 0.8329 (p) REVERT: A 422 MET cc_start: 0.7414 (ttm) cc_final: 0.7189 (ttt) REVERT: E 139 CYS cc_start: 0.7509 (t) cc_final: 0.7111 (t) REVERT: E 195 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.3744 (m-10) REVERT: E 243 MET cc_start: 0.8167 (tpp) cc_final: 0.7511 (tpp) REVERT: E 247 MET cc_start: 0.8134 (mmm) cc_final: 0.7584 (tmm) REVERT: E 258 TRP cc_start: 0.8577 (m100) cc_final: 0.7854 (m100) REVERT: E 310 LEU cc_start: 0.8129 (mt) cc_final: 0.7757 (mt) REVERT: B 87 GLU cc_start: 0.7196 (tp30) cc_final: 0.6588 (tp30) REVERT: B 212 SER cc_start: 0.8695 (m) cc_final: 0.8325 (p) REVERT: B 422 MET cc_start: 0.7408 (ttm) cc_final: 0.7175 (ttt) REVERT: B 516 ASP cc_start: 0.6855 (m-30) cc_final: 0.6552 (m-30) REVERT: B 624 MET cc_start: 0.8229 (ptp) cc_final: 0.7623 (mtm) REVERT: C 66 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7319 (tmm) REVERT: C 87 GLU cc_start: 0.7229 (tp30) cc_final: 0.6615 (tp30) REVERT: C 212 SER cc_start: 0.8698 (m) cc_final: 0.8330 (p) REVERT: C 422 MET cc_start: 0.7407 (ttm) cc_final: 0.7170 (ttt) REVERT: C 516 ASP cc_start: 0.6844 (m-30) cc_final: 0.6556 (m-30) REVERT: C 624 MET cc_start: 0.8232 (ptp) cc_final: 0.7632 (mtm) REVERT: D 87 GLU cc_start: 0.7209 (tp30) cc_final: 0.6608 (tp30) REVERT: D 212 SER cc_start: 0.8697 (m) cc_final: 0.8322 (p) REVERT: D 422 MET cc_start: 0.7422 (ttm) cc_final: 0.7192 (ttt) REVERT: D 516 ASP cc_start: 0.6885 (m-30) cc_final: 0.6652 (m-30) REVERT: F 53 MET cc_start: 0.8202 (ptp) cc_final: 0.7938 (ptp) REVERT: F 139 CYS cc_start: 0.7543 (t) cc_final: 0.7209 (t) REVERT: F 195 TYR cc_start: 0.6397 (OUTLIER) cc_final: 0.3572 (m-10) REVERT: F 243 MET cc_start: 0.8164 (tpp) cc_final: 0.7496 (tpp) REVERT: F 247 MET cc_start: 0.8099 (mmm) cc_final: 0.7551 (tmm) REVERT: F 258 TRP cc_start: 0.8541 (m100) cc_final: 0.7891 (m100) REVERT: F 310 LEU cc_start: 0.8129 (mt) cc_final: 0.7784 (mt) REVERT: G 53 MET cc_start: 0.8217 (ptp) cc_final: 0.7979 (ptp) REVERT: G 139 CYS cc_start: 0.7514 (t) cc_final: 0.7121 (t) REVERT: G 195 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.3550 (m-10) REVERT: G 243 MET cc_start: 0.8119 (tpp) cc_final: 0.7434 (tpp) REVERT: G 247 MET cc_start: 0.8191 (mmm) cc_final: 0.7792 (tmm) REVERT: G 258 TRP cc_start: 0.8581 (m100) cc_final: 0.7864 (m100) REVERT: H 53 MET cc_start: 0.8208 (ptp) cc_final: 0.7937 (ptp) REVERT: H 139 CYS cc_start: 0.7516 (t) cc_final: 0.7125 (t) REVERT: H 195 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.3500 (m-10) REVERT: H 243 MET cc_start: 0.8151 (tpp) cc_final: 0.7483 (tpp) REVERT: H 247 MET cc_start: 0.8054 (mmm) cc_final: 0.7518 (tmm) REVERT: H 258 TRP cc_start: 0.8590 (m100) cc_final: 0.7876 (m100) REVERT: H 310 LEU cc_start: 0.8131 (mt) cc_final: 0.7779 (mt) outliers start: 43 outliers final: 36 residues processed: 371 average time/residue: 0.2057 time to fit residues: 128.1771 Evaluate side-chains 387 residues out of total 3548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 346 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 460 TYR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 305 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 460 TYR Chi-restraints excluded: chain C residue 507 GLN Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 244 HIS Chi-restraints excluded: chain F residue 305 CYS Chi-restraints excluded: chain G residue 195 TYR Chi-restraints excluded: chain H residue 195 TYR Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 53 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 376 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 366 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 HIS G 244 HIS H 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.070973 restraints weight = 75540.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.070627 restraints weight = 66221.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.071179 restraints weight = 56130.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.071451 restraints weight = 46020.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.071488 restraints weight = 43276.397| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33596 Z= 0.174 Angle : 0.564 8.714 45440 Z= 0.283 Chirality : 0.039 0.138 5080 Planarity : 0.003 0.032 5652 Dihedral : 10.127 146.514 4908 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.27 % Allowed : 15.14 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.14), residues: 3928 helix: 2.19 (0.10), residues: 2548 sheet: -0.41 (0.41), residues: 160 loop : 0.02 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 208 TYR 0.016 0.001 TYR B 524 PHE 0.033 0.002 PHE E 336 TRP 0.071 0.002 TRP F 211 HIS 0.010 0.001 HIS F 244 Details of bonding type rmsd covalent geometry : bond 0.00409 (33576) covalent geometry : angle 0.56345 (45420) SS BOND : bond 0.00348 ( 4) SS BOND : angle 0.73414 ( 8) hydrogen bonds : bond 0.04238 ( 1892) hydrogen bonds : angle 3.57291 ( 5448) metal coordination : bond 0.00407 ( 16) metal coordination : angle 1.11664 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4624.33 seconds wall clock time: 81 minutes 21.15 seconds (4881.15 seconds total)