Starting phenix.real_space_refine on Sun Jul 5 14:07:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3m_47490/07_2026/9e3m_47490_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3m_47490/07_2026/9e3m_47490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e3m_47490/07_2026/9e3m_47490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3m_47490/07_2026/9e3m_47490.map" model { file = "/net/cci-nas-00/data/ceres_data/9e3m_47490/07_2026/9e3m_47490_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3m_47490/07_2026/9e3m_47490_trim.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 8 Type Number sf(0) Gaussians Zn 6 6.06 5 P 6 5.49 5 S 111 5.16 5 Na 1 4.78 5 C 9051 2.51 5 N 2295 2.21 5 O 2683 1.98 5 H 12639 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26792 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 8623 Classifications: {'peptide': 546} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 517} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 8623 Classifications: {'peptide': 546} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 517} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 8623 Classifications: {'peptide': 546} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 517} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 183 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {' ZN': 2, 'NAG': 2, 'PLM': 7, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PLM:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 183 Unusual residues: {' ZN': 2, 'NAG': 2, 'PLM': 7, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PLM:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 183 Unusual residues: {' ZN': 2, 'NAG': 2, 'PLM': 7, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PLM:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6777 SG CYS A 479 19.762 51.553 16.352 1.00 72.53 S ATOM 7068 SG CYS A 499 22.779 52.434 18.508 1.00 68.67 S ATOM 7178 SG CYS A 506 23.244 50.821 15.110 1.00 71.09 S ATOM 8225 SG CYS A 572 22.367 48.774 17.962 1.00 69.58 S ATOM 6749 SG CYS A 477 16.157 50.919 17.016 1.00 73.05 S ATOM 6777 SG CYS A 479 19.762 51.553 16.352 1.00 72.53 S ATOM 6806 SG CYS A 482 18.659 48.346 18.210 1.00 72.73 S ATOM 7057 SG CYS A 498 18.736 51.826 19.822 1.00 69.72 S ATOM 15400 SG CYS C 479 65.572 70.465 16.617 1.00 72.53 S ATOM 15691 SG CYS C 499 64.821 67.392 18.743 1.00 68.67 S ATOM 15801 SG CYS C 506 63.207 67.823 15.341 1.00 71.09 S ATOM 16848 SG CYS C 572 61.857 69.580 18.202 1.00 69.58 S ATOM 15372 SG CYS C 477 66.818 73.900 17.317 1.00 73.05 S ATOM 15400 SG CYS C 479 65.572 70.465 16.617 1.00 72.53 S ATOM 15429 SG CYS C 482 63.334 73.005 18.486 1.00 72.73 S ATOM 15680 SG CYS C 498 66.304 71.188 20.097 1.00 69.72 S ATOM 24023 SG CYS B 479 58.911 21.489 16.422 1.00 72.53 S ATOM 24314 SG CYS B 499 56.615 23.657 18.557 1.00 68.67 S ATOM 24424 SG CYS B 506 57.812 24.871 15.172 1.00 71.09 S ATOM 25471 SG CYS B 572 59.994 25.135 18.046 1.00 69.58 S ATOM 23995 SG CYS B 477 61.259 18.687 17.106 1.00 73.05 S ATOM 24023 SG CYS B 479 58.911 21.489 16.422 1.00 72.53 S ATOM 24052 SG CYS B 482 62.220 22.140 18.313 1.00 72.73 S ATOM 24303 SG CYS B 498 59.154 20.461 19.893 1.00 69.72 S Time building chain proxies: 4.46, per 1000 atoms: 0.17 Number of scatterers: 26792 At special positions: 0 Unit cell: (91.368, 97.2, 162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 S 111 16.00 P 6 15.00 Na 1 11.00 O 2683 8.00 N 2295 7.00 C 9051 6.00 H 12639 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.05 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.05 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.05 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 269 " 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=21, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 704 " - " ASN A 202 " " NAG A 705 " - " ASN A 213 " " NAG B 704 " - " ASN B 202 " " NAG B 705 " - " ASN B 213 " " NAG C 704 " - " ASN C 202 " " NAG C 705 " - " ASN C 213 " " NAG D 1 " - " ASN A 187 " " NAG E 1 " - " ASN A 241 " " NAG F 1 " - " ASN C 187 " " NAG G 1 " - " ASN C 241 " " NAG H 1 " - " ASN B 187 " " NAG I 1 " - " ASN B 241 " Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 714.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 506 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 499 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 479 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 572 " pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 479 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 498 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 482 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 477 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 506 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 499 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 479 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 572 " pdb=" ZN B 703 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 479 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 498 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 482 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 477 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 506 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 499 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 479 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 572 " pdb=" ZN C 703 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 479 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 498 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 482 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 477 " Number of angles added : 36 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 21 sheets defined 37.1% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 removed outlier: 3.557A pdb=" N PHE A 11 " --> pdb=" O CYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 49 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.548A pdb=" N CYS A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.708A pdb=" N ILE A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 329 through 342 removed outlier: 4.556A pdb=" N SER A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 378 through 387 removed outlier: 4.261A pdb=" N TYR A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 4.402A pdb=" N CYS A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 510 through 517 removed outlier: 3.618A pdb=" N ARG A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 531 removed outlier: 3.853A pdb=" N GLN A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 559 Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.557A pdb=" N PHE C 11 " --> pdb=" O CYS C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing helix chain 'C' and resid 23 through 49 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 131 through 135 removed outlier: 3.547A pdb=" N CYS C 135 " --> pdb=" O ASP C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.708A pdb=" N ILE C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 329 through 342 removed outlier: 4.556A pdb=" N SER C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 359 Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 374 through 377 Processing helix chain 'C' and resid 378 through 387 removed outlier: 4.261A pdb=" N TYR C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.403A pdb=" N CYS C 493 " --> pdb=" O GLU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 506 through 509 Processing helix chain 'C' and resid 510 through 517 removed outlier: 3.618A pdb=" N ARG C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 531 removed outlier: 3.853A pdb=" N GLN C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 559 Processing helix chain 'C' and resid 560 through 565 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.557A pdb=" N PHE B 11 " --> pdb=" O CYS B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 7 through 11' Processing helix chain 'B' and resid 23 through 49 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.548A pdb=" N CYS B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.708A pdb=" N ILE B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 329 through 342 removed outlier: 4.556A pdb=" N SER B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 359 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 374 through 377 Processing helix chain 'B' and resid 378 through 387 removed outlier: 4.261A pdb=" N TYR B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 removed outlier: 4.403A pdb=" N CYS B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 506 through 509 Processing helix chain 'B' and resid 510 through 517 removed outlier: 3.618A pdb=" N ARG B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 531 removed outlier: 3.853A pdb=" N GLN B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 559 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 570 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.505A pdb=" N VAL C 18 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE B 391 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ARG C 20 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 388 through 392 removed outlier: 6.702A pdb=" N VAL A 18 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE C 391 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG A 20 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 156 removed outlier: 9.131A pdb=" N ILE A 147 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TRP A 167 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR A 149 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N SER A 165 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ARG A 151 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A 313 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE A 108 " --> pdb=" O LYS A 311 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS A 311 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS A 110 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 309 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU A 112 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG A 307 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLN A 114 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLU A 305 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 299 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 66 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 66 Processing sheet with id=AA7, first strand: chain 'A' and resid 69 through 73 Processing sheet with id=AA8, first strand: chain 'A' and resid 388 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 398 through 402 Processing sheet with id=AB1, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AB2, first strand: chain 'C' and resid 147 through 156 removed outlier: 9.131A pdb=" N ILE C 147 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N TRP C 167 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR C 149 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N SER C 165 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ARG C 151 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE C 313 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE C 108 " --> pdb=" O LYS C 311 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS C 311 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS C 110 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 309 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU C 112 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG C 307 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLN C 114 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU C 305 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 299 " --> pdb=" O LYS C 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 66 Processing sheet with id=AB4, first strand: chain 'C' and resid 58 through 66 Processing sheet with id=AB5, first strand: chain 'C' and resid 69 through 73 Processing sheet with id=AB6, first strand: chain 'C' and resid 398 through 402 Processing sheet with id=AB7, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AB8, first strand: chain 'B' and resid 147 through 156 removed outlier: 9.131A pdb=" N ILE B 147 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TRP B 167 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR B 149 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER B 165 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ARG B 151 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE B 313 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE B 108 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS B 311 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS B 110 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 309 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU B 112 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG B 307 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLN B 114 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU B 305 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 299 " --> pdb=" O LYS B 306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 58 through 66 Processing sheet with id=AC1, first strand: chain 'B' and resid 58 through 66 Processing sheet with id=AC2, first strand: chain 'B' and resid 69 through 73 Processing sheet with id=AC3, first strand: chain 'B' and resid 398 through 402 602 hydrogen bonds defined for protein. 1644 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: 5.11 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 12501 1.02 - 1.22: 144 1.22 - 1.42: 6030 1.42 - 1.62: 8205 1.62 - 1.82: 135 Bond restraints: 27015 Sorted by residual: bond pdb=" CA CYS B 373 " pdb=" HA CYS B 373 " ideal model delta sigma weight residual 0.970 1.137 -0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" CA CYS C 373 " pdb=" HA CYS C 373 " ideal model delta sigma weight residual 0.970 1.137 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" CA CYS A 373 " pdb=" HA CYS A 373 " ideal model delta sigma weight residual 0.970 1.136 -0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" CA CYS C 362 " pdb=" HA CYS C 362 " ideal model delta sigma weight residual 0.970 1.136 -0.166 2.00e-02 2.50e+03 6.87e+01 bond pdb=" CA CYS A 362 " pdb=" HA CYS A 362 " ideal model delta sigma weight residual 0.970 1.135 -0.165 2.00e-02 2.50e+03 6.83e+01 ... (remaining 27010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.09: 48021 7.09 - 14.18: 48 14.18 - 21.27: 0 21.27 - 28.36: 6 28.36 - 35.45: 21 Bond angle restraints: 48096 Sorted by residual: angle pdb=" N ARG A 364 " pdb=" CA ARG A 364 " pdb=" HA ARG A 364 " ideal model delta sigma weight residual 110.00 74.55 35.45 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N ARG C 364 " pdb=" CA ARG C 364 " pdb=" HA ARG C 364 " ideal model delta sigma weight residual 110.00 74.56 35.44 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N ARG B 364 " pdb=" CA ARG B 364 " pdb=" HA ARG B 364 " ideal model delta sigma weight residual 110.00 74.59 35.41 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C ARG B 364 " pdb=" CA ARG B 364 " pdb=" HA ARG B 364 " ideal model delta sigma weight residual 109.00 74.13 34.87 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C ARG C 364 " pdb=" CA ARG C 364 " pdb=" HA ARG C 364 " ideal model delta sigma weight residual 109.00 74.14 34.86 3.00e+00 1.11e-01 1.35e+02 ... (remaining 48091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.75: 12535 23.75 - 47.51: 791 47.51 - 71.26: 198 71.26 - 95.02: 33 95.02 - 118.77: 9 Dihedral angle restraints: 13566 sinusoidal: 7653 harmonic: 5913 Sorted by residual: dihedral pdb=" O2B GDP B 701 " pdb=" O3A GDP B 701 " pdb=" PB GDP B 701 " pdb=" PA GDP B 701 " ideal model delta sinusoidal sigma weight residual -180.00 -61.23 -118.77 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" O2B GDP C 701 " pdb=" O3A GDP C 701 " pdb=" PB GDP C 701 " pdb=" PA GDP C 701 " ideal model delta sinusoidal sigma weight residual -180.00 -61.25 -118.75 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" O2B GDP A 701 " pdb=" O3A GDP A 701 " pdb=" PB GDP A 701 " pdb=" PA GDP A 701 " ideal model delta sinusoidal sigma weight residual -180.00 -61.26 -118.74 1 2.00e+01 2.50e-03 3.55e+01 ... (remaining 13563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1899 0.087 - 0.175: 210 0.175 - 0.262: 3 0.262 - 0.349: 0 0.349 - 0.436: 6 Chirality restraints: 2118 Sorted by residual: chirality pdb=" CA ARG B 364 " pdb=" N ARG B 364 " pdb=" C ARG B 364 " pdb=" CB ARG B 364 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ARG A 364 " pdb=" N ARG A 364 " pdb=" C ARG A 364 " pdb=" CB ARG A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ARG C 364 " pdb=" N ARG C 364 " pdb=" C ARG C 364 " pdb=" CB ARG C 364 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 2115 not shown) Planarity restraints: 3924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 704 " -0.335 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG B 704 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B 704 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG B 704 " 0.512 2.00e-02 2.50e+03 pdb=" O7 NAG B 704 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 704 " 0.335 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG C 704 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 704 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG C 704 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG C 704 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " 0.335 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG A 704 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " 0.113 2.00e-02 2.50e+03 ... (remaining 3921 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 1001 2.14 - 2.75: 47269 2.75 - 3.37: 74540 3.37 - 3.98: 103449 3.98 - 4.60: 156583 Nonbonded interactions: 382842 Sorted by model distance: nonbonded pdb=" O LEU A 287 " pdb=" HZ1 LYS B 193 " model vdw 1.519 2.450 nonbonded pdb=" H ARG A 364 " pdb=" HA ARG A 364 " model vdw 1.572 1.816 nonbonded pdb=" H ARG C 364 " pdb=" HA ARG C 364 " model vdw 1.572 1.816 nonbonded pdb=" H ARG B 364 " pdb=" HA ARG B 364 " model vdw 1.572 1.816 nonbonded pdb=" HZ1 LYS C 193 " pdb=" O LEU B 287 " model vdw 1.572 2.450 ... (remaining 382837 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 6 through 714) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.090 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: 0.180 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.420 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.009 0.076 14451 Z= 0.434 Angle : 1.007 13.671 19536 Z= 0.504 Chirality : 0.056 0.436 2118 Planarity : 0.013 0.289 2391 Dihedral : 16.562 118.772 5997 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.81 % Allowed : 15.48 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.05 (0.21), residues: 1620 helix: 0.38 (0.25), residues: 462 sheet: -0.21 (0.24), residues: 429 loop : 0.16 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 294 TYR 0.013 0.002 TYR C 358 PHE 0.018 0.002 PHE C 102 TRP 0.019 0.002 TRP A 575 HIS 0.003 0.001 HIS C 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.41 (14376) covalent geometry : angle 0.95623 / 0.50 (19422) SS BOND : bond 0.01138 / 0.72 ( 12) SS BOND : angle 2.11531 / 1.36 ( 24) hydrogen bonds : bond 0.17797 / 12.28 ( 572) hydrogen bonds : angle 7.89538 / 5.56 ( 1644) metal coordination : bond 0.01563 / 1.06 ( 24) metal coordination : angle 5.62249 / 3.50 ( 36) Misc. bond : bond 0.03423 / 2.27 ( 21) link_BETA1-4 : bond 0.00637 / 0.34 ( 6) link_BETA1-4 : angle 2.40830 / 1.43 ( 18) link_NAG-ASN : bond 0.02192 / 1.38 ( 12) link_NAG-ASN : angle 4.35548 / 2.84 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7871 (ttm170) cc_final: 0.7643 (ttp80) REVERT: A 551 ARG cc_start: 0.6749 (mmt90) cc_final: 0.6327 (mtp-110) REVERT: A 561 GLN cc_start: 0.7372 (pt0) cc_final: 0.7002 (tt0) REVERT: C 32 PHE cc_start: 0.7505 (t80) cc_final: 0.7260 (t80) REVERT: C 53 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7553 (ttp80) REVERT: C 551 ARG cc_start: 0.6638 (mmt90) cc_final: 0.6175 (mtp-110) REVERT: C 589 SER cc_start: 0.8109 (t) cc_final: 0.7651 (m) REVERT: B 32 PHE cc_start: 0.7565 (t80) cc_final: 0.7250 (t80) REVERT: B 53 ARG cc_start: 0.7819 (ttm170) cc_final: 0.7529 (ttp80) REVERT: B 521 HIS cc_start: 0.6964 (m-70) cc_final: 0.6510 (m90) REVERT: B 551 ARG cc_start: 0.6655 (mmt90) cc_final: 0.6236 (mtp-110) REVERT: B 589 SER cc_start: 0.8142 (t) cc_final: 0.7719 (m) outliers start: 12 outliers final: 11 residues processed: 192 average time/residue: 1.2465 time to fit residues: 262.7324 Evaluate side-chains 163 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.177215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124653 restraints weight = 34265.785| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.71 r_work: 0.3339 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14451 Z= 0.145 Angle : 0.624 6.898 19536 Z= 0.304 Chirality : 0.045 0.355 2118 Planarity : 0.004 0.039 2391 Dihedral : 10.339 138.344 2823 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.10 % Allowed : 16.50 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.16 (0.21), residues: 1620 helix: 1.12 (0.26), residues: 438 sheet: -0.42 (0.23), residues: 420 loop : -0.04 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 500 TYR 0.011 0.001 TYR C 288 PHE 0.010 0.001 PHE A 235 TRP 0.010 0.001 TRP C 575 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14376) covalent geometry : angle 0.58131 / 0.30 (19422) SS BOND : bond 0.00456 / 0.31 ( 12) SS BOND : angle 1.86977 / 1.35 ( 24) hydrogen bonds : bond 0.04752 / 3.18 ( 572) hydrogen bonds : angle 6.18562 / 4.36 ( 1644) metal coordination : bond 0.00519 / 0.37 ( 24) metal coordination : angle 4.36429 / 2.89 ( 36) Misc. bond : bond 0.00037 / 0.02 ( 21) link_BETA1-4 : bond 0.00081 / 0.04 ( 6) link_BETA1-4 : angle 1.63291 / 0.93 ( 18) link_NAG-ASN : bond 0.00543 / 0.33 ( 12) link_NAG-ASN : angle 2.44258 / 1.60 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8467 (ttm170) cc_final: 0.7933 (ttp80) REVERT: A 551 ARG cc_start: 0.7514 (mmt90) cc_final: 0.7159 (mtp-110) REVERT: A 561 GLN cc_start: 0.7782 (pt0) cc_final: 0.7517 (tt0) REVERT: C 53 ARG cc_start: 0.8324 (ttm170) cc_final: 0.7798 (ttp80) REVERT: C 356 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: C 589 SER cc_start: 0.8121 (t) cc_final: 0.7621 (m) REVERT: B 32 PHE cc_start: 0.7925 (t80) cc_final: 0.7634 (t80) REVERT: B 53 ARG cc_start: 0.8333 (ttm170) cc_final: 0.7757 (ttp80) REVERT: B 356 ASP cc_start: 0.7531 (t70) cc_final: 0.7299 (m-30) REVERT: B 589 SER cc_start: 0.8132 (t) cc_final: 0.7621 (m) outliers start: 31 outliers final: 20 residues processed: 179 average time/residue: 1.1484 time to fit residues: 228.0792 Evaluate side-chains 177 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 5 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.174719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121394 restraints weight = 34213.294| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.71 r_work: 0.3303 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14451 Z= 0.171 Angle : 0.582 6.266 19536 Z= 0.287 Chirality : 0.045 0.370 2118 Planarity : 0.004 0.048 2391 Dihedral : 9.514 151.118 2821 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.38 % Allowed : 16.16 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.13 (0.21), residues: 1620 helix: 1.08 (0.25), residues: 447 sheet: -0.47 (0.24), residues: 420 loop : -0.04 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 264 TYR 0.011 0.001 TYR C 40 PHE 0.015 0.001 PHE A 275 TRP 0.009 0.001 TRP C 575 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (14376) covalent geometry : angle 0.54910 / 0.28 (19422) SS BOND : bond 0.00512 / 0.34 ( 12) SS BOND : angle 1.80068 / 1.25 ( 24) hydrogen bonds : bond 0.04200 / 2.83 ( 572) hydrogen bonds : angle 5.75913 / 4.07 ( 1644) metal coordination : bond 0.00557 / 0.39 ( 24) metal coordination : angle 3.67189 / 2.37 ( 36) Misc. bond : bond 0.00050 / 0.03 ( 21) link_BETA1-4 : bond 0.00108 / 0.06 ( 6) link_BETA1-4 : angle 1.62542 / 0.97 ( 18) link_NAG-ASN : bond 0.00436 / 0.26 ( 12) link_NAG-ASN : angle 2.06684 / 1.39 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8488 (ttm170) cc_final: 0.7963 (ttp80) REVERT: A 551 ARG cc_start: 0.7533 (mmt90) cc_final: 0.7031 (mtm110) REVERT: A 589 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7380 (m) REVERT: C 53 ARG cc_start: 0.8439 (ttm170) cc_final: 0.7829 (ttp80) REVERT: C 589 SER cc_start: 0.8171 (t) cc_final: 0.7675 (m) REVERT: B 32 PHE cc_start: 0.7949 (t80) cc_final: 0.7627 (t80) REVERT: B 53 ARG cc_start: 0.8463 (ttm170) cc_final: 0.7875 (ttp80) REVERT: B 589 SER cc_start: 0.8126 (t) cc_final: 0.7605 (m) outliers start: 35 outliers final: 24 residues processed: 183 average time/residue: 1.2616 time to fit residues: 255.0685 Evaluate side-chains 179 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 161 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.173786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120306 restraints weight = 34069.022| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.71 r_work: 0.3288 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14451 Z= 0.163 Angle : 0.575 6.894 19536 Z= 0.282 Chirality : 0.045 0.373 2118 Planarity : 0.004 0.059 2391 Dihedral : 9.068 145.642 2821 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.44 % Allowed : 16.09 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.25 (0.21), residues: 1620 helix: 1.19 (0.25), residues: 444 sheet: -0.52 (0.24), residues: 420 loop : 0.12 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 514 TYR 0.011 0.001 TYR C 40 PHE 0.014 0.001 PHE B 275 TRP 0.009 0.001 TRP B 575 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (14376) covalent geometry : angle 0.54127 / 0.28 (19422) SS BOND : bond 0.00499 / 0.36 ( 12) SS BOND : angle 1.75948 / 1.22 ( 24) hydrogen bonds : bond 0.03861 / 2.60 ( 572) hydrogen bonds : angle 5.52549 / 3.92 ( 1644) metal coordination : bond 0.00491 / 0.34 ( 24) metal coordination : angle 3.73259 / 2.40 ( 36) Misc. bond : bond 0.00025 / 0.02 ( 21) link_BETA1-4 : bond 0.00078 / 0.04 ( 6) link_BETA1-4 : angle 1.57642 / 0.95 ( 18) link_NAG-ASN : bond 0.00368 / 0.23 ( 12) link_NAG-ASN : angle 2.03289 / 1.37 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8470 (ttm170) cc_final: 0.7966 (ttp80) REVERT: A 217 THR cc_start: 0.8543 (m) cc_final: 0.8334 (t) REVERT: A 521 HIS cc_start: 0.7440 (m-70) cc_final: 0.7120 (m90) REVERT: A 551 ARG cc_start: 0.7609 (mmt90) cc_final: 0.7187 (mtm110) REVERT: A 589 SER cc_start: 0.8122 (OUTLIER) cc_final: 0.7452 (m) REVERT: C 53 ARG cc_start: 0.8438 (ttm170) cc_final: 0.7899 (ttp80) REVERT: C 551 ARG cc_start: 0.7539 (mmt90) cc_final: 0.7050 (mtm110) REVERT: C 589 SER cc_start: 0.8131 (t) cc_final: 0.7702 (m) REVERT: B 32 PHE cc_start: 0.7927 (t80) cc_final: 0.7598 (t80) REVERT: B 53 ARG cc_start: 0.8455 (ttm170) cc_final: 0.7893 (ttp80) REVERT: B 521 HIS cc_start: 0.7191 (m-70) cc_final: 0.6798 (m90) REVERT: B 551 ARG cc_start: 0.7633 (mmt90) cc_final: 0.7184 (mtm110) REVERT: B 589 SER cc_start: 0.8087 (t) cc_final: 0.7621 (m) outliers start: 36 outliers final: 27 residues processed: 185 average time/residue: 1.1480 time to fit residues: 235.1815 Evaluate side-chains 185 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 371 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.173777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120269 restraints weight = 34063.514| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.71 r_work: 0.3290 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14451 Z= 0.159 Angle : 0.563 6.739 19536 Z= 0.274 Chirality : 0.044 0.378 2118 Planarity : 0.004 0.043 2391 Dihedral : 8.708 132.270 2821 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.31 % Allowed : 16.70 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.38 (0.21), residues: 1620 helix: 1.46 (0.25), residues: 441 sheet: -0.51 (0.24), residues: 420 loop : 0.14 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 514 TYR 0.011 0.001 TYR C 40 PHE 0.013 0.001 PHE A 275 TRP 0.009 0.001 TRP C 575 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (14376) covalent geometry : angle 0.52968 / 0.27 (19422) SS BOND : bond 0.00512 / 0.33 ( 12) SS BOND : angle 1.78406 / 1.25 ( 24) hydrogen bonds : bond 0.03735 / 2.52 ( 572) hydrogen bonds : angle 5.43648 / 3.86 ( 1644) metal coordination : bond 0.00526 / 0.36 ( 24) metal coordination : angle 3.59499 / 2.29 ( 36) Misc. bond : bond 0.00028 / 0.02 ( 21) link_BETA1-4 : bond 0.00097 / 0.05 ( 6) link_BETA1-4 : angle 1.69437 / 1.02 ( 18) link_NAG-ASN : bond 0.00355 / 0.22 ( 12) link_NAG-ASN : angle 1.98630 / 1.34 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.751 Fit side-chains REVERT: A 24 MET cc_start: 0.8153 (mmp) cc_final: 0.7849 (mmm) REVERT: A 53 ARG cc_start: 0.8488 (ttm170) cc_final: 0.7956 (ttp80) REVERT: A 217 THR cc_start: 0.8508 (m) cc_final: 0.8281 (t) REVERT: A 512 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8116 (mp) REVERT: A 521 HIS cc_start: 0.7437 (m-70) cc_final: 0.7115 (m90) REVERT: A 551 ARG cc_start: 0.7606 (mmt90) cc_final: 0.7198 (mtm110) REVERT: A 589 SER cc_start: 0.8054 (t) cc_final: 0.7430 (m) REVERT: C 53 ARG cc_start: 0.8466 (ttm170) cc_final: 0.7906 (ttp80) REVERT: C 551 ARG cc_start: 0.7510 (mmt90) cc_final: 0.7042 (mtm110) REVERT: C 589 SER cc_start: 0.8104 (t) cc_final: 0.7693 (m) REVERT: B 32 PHE cc_start: 0.7938 (t80) cc_final: 0.7608 (t80) REVERT: B 53 ARG cc_start: 0.8462 (ttm170) cc_final: 0.7817 (ttp80) REVERT: B 521 HIS cc_start: 0.7176 (m-70) cc_final: 0.6781 (m90) REVERT: B 551 ARG cc_start: 0.7678 (mmt90) cc_final: 0.7253 (mtm110) REVERT: B 589 SER cc_start: 0.8066 (t) cc_final: 0.7613 (m) outliers start: 34 outliers final: 24 residues processed: 184 average time/residue: 1.3281 time to fit residues: 268.8520 Evaluate side-chains 181 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 371 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.173183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119471 restraints weight = 33898.136| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.71 r_work: 0.3281 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14451 Z= 0.172 Angle : 0.574 6.826 19536 Z= 0.280 Chirality : 0.045 0.379 2118 Planarity : 0.004 0.042 2391 Dihedral : 8.532 118.485 2820 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.51 % Allowed : 16.36 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.40 (0.21), residues: 1620 helix: 1.34 (0.25), residues: 444 sheet: -0.49 (0.24), residues: 420 loop : 0.23 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 514 TYR 0.012 0.001 TYR C 295 PHE 0.014 0.002 PHE B 275 TRP 0.009 0.001 TRP B 575 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (14376) covalent geometry : angle 0.53951 / 0.28 (19422) SS BOND : bond 0.00439 / 0.30 ( 12) SS BOND : angle 1.78308 / 1.25 ( 24) hydrogen bonds : bond 0.03753 / 2.53 ( 572) hydrogen bonds : angle 5.39735 / 3.83 ( 1644) metal coordination : bond 0.00548 / 0.38 ( 24) metal coordination : angle 3.69186 / 2.38 ( 36) Misc. bond : bond 0.00028 / 0.02 ( 21) link_BETA1-4 : bond 0.00120 / 0.06 ( 6) link_BETA1-4 : angle 1.74981 / 1.04 ( 18) link_NAG-ASN : bond 0.00385 / 0.24 ( 12) link_NAG-ASN : angle 2.05672 / 1.39 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.791 Fit side-chains REVERT: A 53 ARG cc_start: 0.8510 (ttm170) cc_final: 0.7956 (ttp80) REVERT: A 217 THR cc_start: 0.8576 (m) cc_final: 0.8338 (t) REVERT: A 512 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8112 (mp) REVERT: A 521 HIS cc_start: 0.7455 (m-70) cc_final: 0.7148 (m90) REVERT: A 551 ARG cc_start: 0.7645 (mmt90) cc_final: 0.7237 (mtm110) REVERT: A 589 SER cc_start: 0.7949 (OUTLIER) cc_final: 0.7385 (m) REVERT: C 53 ARG cc_start: 0.8475 (ttm170) cc_final: 0.7894 (ttp80) REVERT: C 551 ARG cc_start: 0.7550 (mmt90) cc_final: 0.7141 (mtm110) REVERT: C 589 SER cc_start: 0.8078 (t) cc_final: 0.7700 (m) REVERT: B 32 PHE cc_start: 0.7939 (t80) cc_final: 0.7621 (t80) REVERT: B 53 ARG cc_start: 0.8452 (ttm170) cc_final: 0.7819 (ttp80) REVERT: B 521 HIS cc_start: 0.7202 (m-70) cc_final: 0.6828 (m90) REVERT: B 551 ARG cc_start: 0.7712 (mmt90) cc_final: 0.7256 (mtm110) REVERT: B 589 SER cc_start: 0.8022 (t) cc_final: 0.7592 (m) outliers start: 37 outliers final: 24 residues processed: 180 average time/residue: 1.2634 time to fit residues: 251.2854 Evaluate side-chains 181 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 363 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 87 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.171622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117628 restraints weight = 33747.543| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.70 r_work: 0.3264 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14451 Z= 0.235 Angle : 0.623 6.685 19536 Z= 0.305 Chirality : 0.046 0.384 2118 Planarity : 0.004 0.040 2391 Dihedral : 8.847 108.767 2818 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.10 % Allowed : 16.70 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.25 (0.21), residues: 1620 helix: 0.95 (0.25), residues: 465 sheet: -0.46 (0.25), residues: 420 loop : 0.22 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.015 0.002 TYR B 295 PHE 0.019 0.002 PHE C 102 TRP 0.009 0.002 TRP C 31 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (14376) covalent geometry : angle 0.58599 / 0.30 (19422) SS BOND : bond 0.00501 / 0.34 ( 12) SS BOND : angle 2.00417 / 1.41 ( 24) hydrogen bonds : bond 0.04173 / 2.82 ( 572) hydrogen bonds : angle 5.59234 / 3.97 ( 1644) metal coordination : bond 0.00701 / 0.48 ( 24) metal coordination : angle 3.86224 / 2.51 ( 36) Misc. bond : bond 0.00045 / 0.03 ( 21) link_BETA1-4 : bond 0.00269 / 0.13 ( 6) link_BETA1-4 : angle 2.08000 / 1.22 ( 18) link_NAG-ASN : bond 0.00560 / 0.35 ( 12) link_NAG-ASN : angle 2.37670 / 1.61 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.8136 (mmp) cc_final: 0.7833 (mmm) REVERT: A 53 ARG cc_start: 0.8509 (ttm170) cc_final: 0.7951 (ttp80) REVERT: A 512 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8136 (mp) REVERT: A 521 HIS cc_start: 0.7516 (m-70) cc_final: 0.7225 (m90) REVERT: A 551 ARG cc_start: 0.7630 (mmt90) cc_final: 0.7252 (mtm110) REVERT: A 562 ASP cc_start: 0.8067 (m-30) cc_final: 0.7627 (m-30) REVERT: A 589 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7365 (m) REVERT: C 53 ARG cc_start: 0.8500 (ttm170) cc_final: 0.7904 (ttp80) REVERT: C 521 HIS cc_start: 0.7137 (m-70) cc_final: 0.6750 (m90) REVERT: C 551 ARG cc_start: 0.7538 (mmt90) cc_final: 0.7168 (mtm110) REVERT: C 589 SER cc_start: 0.7992 (t) cc_final: 0.7598 (m) REVERT: B 32 PHE cc_start: 0.7982 (t80) cc_final: 0.7692 (t80) REVERT: B 53 ARG cc_start: 0.8446 (ttm170) cc_final: 0.7892 (ttp80) REVERT: B 521 HIS cc_start: 0.7176 (m-70) cc_final: 0.6826 (m90) REVERT: B 551 ARG cc_start: 0.7701 (mmt90) cc_final: 0.7278 (mtm110) REVERT: B 589 SER cc_start: 0.8006 (t) cc_final: 0.7564 (m) outliers start: 31 outliers final: 24 residues processed: 179 average time/residue: 1.3093 time to fit residues: 258.7245 Evaluate side-chains 181 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 363 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 89 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.172905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118947 restraints weight = 33881.687| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.72 r_work: 0.3278 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14451 Z= 0.167 Angle : 0.571 7.039 19536 Z= 0.279 Chirality : 0.045 0.381 2118 Planarity : 0.004 0.041 2391 Dihedral : 8.320 88.831 2818 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.90 % Allowed : 17.11 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.38 (0.21), residues: 1620 helix: 1.24 (0.25), residues: 462 sheet: -0.49 (0.24), residues: 420 loop : 0.24 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 514 TYR 0.012 0.001 TYR C 40 PHE 0.015 0.001 PHE B 102 TRP 0.009 0.001 TRP B 575 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (14376) covalent geometry : angle 0.53715 / 0.27 (19422) SS BOND : bond 0.00442 / 0.30 ( 12) SS BOND : angle 1.76265 / 1.24 ( 24) hydrogen bonds : bond 0.03709 / 2.50 ( 572) hydrogen bonds : angle 5.40042 / 3.83 ( 1644) metal coordination : bond 0.00573 / 0.39 ( 24) metal coordination : angle 3.70428 / 2.35 ( 36) Misc. bond : bond 0.00029 / 0.02 ( 21) link_BETA1-4 : bond 0.00116 / 0.07 ( 6) link_BETA1-4 : angle 1.73826 / 1.03 ( 18) link_NAG-ASN : bond 0.00382 / 0.24 ( 12) link_NAG-ASN : angle 2.05194 / 1.38 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8153 (mmp) cc_final: 0.7850 (mmm) REVERT: A 53 ARG cc_start: 0.8502 (ttm170) cc_final: 0.7952 (ttp80) REVERT: A 217 THR cc_start: 0.8585 (m) cc_final: 0.8351 (t) REVERT: A 512 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8103 (mp) REVERT: A 521 HIS cc_start: 0.7489 (m-70) cc_final: 0.7196 (m90) REVERT: A 551 ARG cc_start: 0.7618 (mmt90) cc_final: 0.7231 (mtm110) REVERT: A 589 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7324 (m) REVERT: C 53 ARG cc_start: 0.8497 (ttm170) cc_final: 0.7903 (ttp80) REVERT: C 521 HIS cc_start: 0.7106 (m-70) cc_final: 0.6733 (m90) REVERT: C 551 ARG cc_start: 0.7529 (mmt90) cc_final: 0.7130 (mtm110) REVERT: C 589 SER cc_start: 0.7983 (t) cc_final: 0.7596 (m) REVERT: B 32 PHE cc_start: 0.7946 (t80) cc_final: 0.7676 (t80) REVERT: B 53 ARG cc_start: 0.8450 (ttm170) cc_final: 0.7903 (ttp80) REVERT: B 521 HIS cc_start: 0.7166 (m-70) cc_final: 0.6831 (m90) REVERT: B 551 ARG cc_start: 0.7713 (mmt90) cc_final: 0.7273 (mtm110) REVERT: B 589 SER cc_start: 0.7984 (t) cc_final: 0.7533 (m) outliers start: 28 outliers final: 21 residues processed: 175 average time/residue: 1.2830 time to fit residues: 248.6474 Evaluate side-chains 175 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 363 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 159 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 111 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.173615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119853 restraints weight = 33590.834| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.71 r_work: 0.3295 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14451 Z= 0.134 Angle : 0.544 6.940 19536 Z= 0.265 Chirality : 0.044 0.379 2118 Planarity : 0.004 0.041 2391 Dihedral : 7.882 67.289 2818 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.90 % Allowed : 16.97 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.45 (0.21), residues: 1620 helix: 1.43 (0.25), residues: 462 sheet: -0.55 (0.24), residues: 420 loop : 0.27 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.014 0.001 TYR B 295 PHE 0.013 0.001 PHE B 102 TRP 0.009 0.001 TRP A 575 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (14376) covalent geometry : angle 0.51094 / 0.26 (19422) SS BOND : bond 0.00537 / 0.40 ( 12) SS BOND : angle 1.67533 / 1.16 ( 24) hydrogen bonds : bond 0.03474 / 2.33 ( 572) hydrogen bonds : angle 5.26634 / 3.74 ( 1644) metal coordination : bond 0.00505 / 0.35 ( 24) metal coordination : angle 3.58173 / 2.27 ( 36) Misc. bond : bond 0.00019 / 0.01 ( 21) link_BETA1-4 : bond 0.00084 / 0.05 ( 6) link_BETA1-4 : angle 1.67502 / 1.00 ( 18) link_NAG-ASN : bond 0.00297 / 0.18 ( 12) link_NAG-ASN : angle 1.84251 / 1.23 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8491 (ttm170) cc_final: 0.7967 (ttp80) REVERT: A 217 THR cc_start: 0.8462 (m) cc_final: 0.8244 (t) REVERT: A 512 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8125 (mp) REVERT: A 521 HIS cc_start: 0.7441 (m-70) cc_final: 0.7146 (m90) REVERT: A 551 ARG cc_start: 0.7607 (mmt90) cc_final: 0.7216 (mtm110) REVERT: A 589 SER cc_start: 0.7861 (t) cc_final: 0.7320 (m) REVERT: C 53 ARG cc_start: 0.8464 (ttm170) cc_final: 0.7884 (ttp80) REVERT: C 521 HIS cc_start: 0.7061 (m-70) cc_final: 0.6718 (m90) REVERT: C 551 ARG cc_start: 0.7550 (mmt90) cc_final: 0.7152 (mtm110) REVERT: C 589 SER cc_start: 0.8042 (t) cc_final: 0.7650 (m) REVERT: B 32 PHE cc_start: 0.7906 (t80) cc_final: 0.7632 (t80) REVERT: B 53 ARG cc_start: 0.8452 (ttm170) cc_final: 0.7918 (ttp80) REVERT: B 72 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7672 (mttp) REVERT: B 521 HIS cc_start: 0.7148 (m-70) cc_final: 0.6820 (m90) REVERT: B 551 ARG cc_start: 0.7660 (mmt90) cc_final: 0.7244 (mtm110) REVERT: B 589 SER cc_start: 0.7980 (t) cc_final: 0.7530 (m) outliers start: 28 outliers final: 23 residues processed: 178 average time/residue: 1.2828 time to fit residues: 252.7543 Evaluate side-chains 182 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 363 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 130 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.173450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119447 restraints weight = 33533.400| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.72 r_work: 0.3288 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14451 Z= 0.147 Angle : 0.551 6.675 19536 Z= 0.269 Chirality : 0.044 0.381 2118 Planarity : 0.004 0.041 2391 Dihedral : 7.844 62.451 2818 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.56 % Allowed : 17.52 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.47 (0.21), residues: 1620 helix: 1.46 (0.25), residues: 462 sheet: -0.56 (0.24), residues: 420 loop : 0.28 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.011 0.001 TYR A 40 PHE 0.015 0.001 PHE B 102 TRP 0.009 0.001 TRP C 575 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14376) covalent geometry : angle 0.51841 / 0.26 (19422) SS BOND : bond 0.00461 / 0.30 ( 12) SS BOND : angle 1.74244 / 1.24 ( 24) hydrogen bonds : bond 0.03534 / 2.37 ( 572) hydrogen bonds : angle 5.25277 / 3.73 ( 1644) metal coordination : bond 0.00527 / 0.36 ( 24) metal coordination : angle 3.58584 / 2.29 ( 36) Misc. bond : bond 0.00024 / 0.02 ( 21) link_BETA1-4 : bond 0.00080 / 0.05 ( 6) link_BETA1-4 : angle 1.70011 / 1.02 ( 18) link_NAG-ASN : bond 0.00318 / 0.20 ( 12) link_NAG-ASN : angle 1.90553 / 1.28 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 360 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.8156 (mmp) cc_final: 0.7844 (mmm) REVERT: A 53 ARG cc_start: 0.8506 (ttm170) cc_final: 0.7972 (ttp80) REVERT: A 217 THR cc_start: 0.8499 (m) cc_final: 0.8285 (t) REVERT: A 512 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 521 HIS cc_start: 0.7452 (m-70) cc_final: 0.7201 (m90) REVERT: A 551 ARG cc_start: 0.7617 (mmt90) cc_final: 0.7222 (mtm110) REVERT: A 589 SER cc_start: 0.7891 (t) cc_final: 0.7330 (m) REVERT: C 53 ARG cc_start: 0.8480 (ttm170) cc_final: 0.7898 (ttp80) REVERT: C 521 HIS cc_start: 0.7035 (m-70) cc_final: 0.6702 (m90) REVERT: C 551 ARG cc_start: 0.7570 (mmt90) cc_final: 0.7168 (mtm110) REVERT: C 589 SER cc_start: 0.8071 (t) cc_final: 0.7673 (m) REVERT: B 32 PHE cc_start: 0.7924 (t80) cc_final: 0.7651 (t80) REVERT: B 53 ARG cc_start: 0.8448 (ttm170) cc_final: 0.7910 (ttp80) REVERT: B 521 HIS cc_start: 0.7147 (m-70) cc_final: 0.6829 (m90) REVERT: B 551 ARG cc_start: 0.7684 (mmt90) cc_final: 0.7259 (mtm110) REVERT: B 589 SER cc_start: 0.7989 (t) cc_final: 0.7531 (m) outliers start: 23 outliers final: 23 residues processed: 178 average time/residue: 1.2875 time to fit residues: 254.3582 Evaluate side-chains 182 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 363 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 152 optimal weight: 0.5980 chunk 135 optimal weight: 0.0970 chunk 160 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 153 optimal weight: 0.0000 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 102 optimal weight: 0.8980 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121580 restraints weight = 33523.463| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.73 r_work: 0.3316 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14451 Z= 0.103 Angle : 0.517 6.686 19536 Z= 0.252 Chirality : 0.044 0.377 2118 Planarity : 0.004 0.042 2391 Dihedral : 7.416 59.927 2818 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.43 % Allowed : 17.79 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.56 (0.21), residues: 1620 helix: 1.62 (0.25), residues: 462 sheet: -0.60 (0.24), residues: 420 loop : 0.33 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.008 0.001 TYR B 40 PHE 0.011 0.001 PHE B 102 TRP 0.008 0.001 TRP A 575 HIS 0.001 0.000 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (14376) covalent geometry : angle 0.48742 / 0.25 (19422) SS BOND : bond 0.00406 / 0.28 ( 12) SS BOND : angle 1.59732 / 1.11 ( 24) hydrogen bonds : bond 0.03199 / 2.14 ( 572) hydrogen bonds : angle 5.07181 / 3.61 ( 1644) metal coordination : bond 0.00439 / 0.30 ( 24) metal coordination : angle 3.41212 / 2.15 ( 36) Misc. bond : bond 0.00014 / 0.01 ( 21) link_BETA1-4 : bond 0.00158 / 0.09 ( 6) link_BETA1-4 : angle 1.40656 / 0.87 ( 18) link_NAG-ASN : bond 0.00180 / 0.11 ( 12) link_NAG-ASN : angle 1.60468 / 1.06 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10603.48 seconds wall clock time: 180 minutes 15.43 seconds (10815.43 seconds total)