Starting phenix.real_space_refine on Fri Feb 6 21:31:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3m_47490/02_2026/9e3m_47490_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3m_47490/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9e3m_47490/02_2026/9e3m_47490_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3m_47490/02_2026/9e3m_47490_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e3m_47490/02_2026/9e3m_47490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3m_47490/02_2026/9e3m_47490.map" } 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-2.0-5952/lib/python3.9/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, 184 Unusual residues: {' NA': 1, ' ZN': 2, 'NAG': 2, 'PLM': 7, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} 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: 4.91, per 1000 atoms: 0.18 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: 2.40 Conformation dependent library (CDL) restraints added in 798.8 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: 0.76 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: 6.43 Time building geometry restraints manager: 3.28 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: 14.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 31.880 Find NCS groups from input model: 0.520 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 covalent geometry : bond 0.00909 (14376) covalent geometry : angle 0.95623 (19422) SS BOND : bond 0.01138 ( 12) SS BOND : angle 2.11531 ( 24) hydrogen bonds : bond 0.17797 ( 572) hydrogen bonds : angle 7.89538 ( 1644) metal coordination : bond 0.01563 ( 24) metal coordination : angle 5.62249 ( 36) Misc. bond : bond 0.03423 ( 21) link_BETA1-4 : bond 0.00637 ( 6) link_BETA1-4 : angle 2.40830 ( 18) link_NAG-ASN : bond 0.02192 ( 12) link_NAG-ASN : angle 4.35548 ( 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 : 0.747 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: 1.5114 time to fit residues: 314.2256 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 : 0.718 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.177126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124582 restraints weight = 34289.582| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.70 r_work: 0.3340 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: 0.8230 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14451 Z= 0.150 Angle : 0.622 6.813 19536 Z= 0.303 Chirality : 0.045 0.355 2118 Planarity : 0.005 0.040 2391 Dihedral : 10.296 139.282 2823 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 1.13 (0.26), residues: 438 sheet: -0.43 (0.23), residues: 420 loop : -0.03 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 294 TYR 0.010 0.001 TYR C 288 PHE 0.011 0.001 PHE A 235 TRP 0.010 0.001 TRP C 575 HIS 0.002 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00328 (14376) covalent geometry : angle 0.58145 (19422) SS BOND : bond 0.00458 ( 12) SS BOND : angle 1.82269 ( 24) hydrogen bonds : bond 0.04869 ( 572) hydrogen bonds : angle 6.16260 ( 1644) metal coordination : bond 0.00539 ( 24) metal coordination : angle 4.31241 ( 36) Misc. bond : bond 0.00052 ( 21) link_BETA1-4 : bond 0.00104 ( 6) link_BETA1-4 : angle 1.65526 ( 18) link_NAG-ASN : bond 0.00738 ( 12) link_NAG-ASN : angle 2.32983 ( 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 189 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8463 (ttm170) cc_final: 0.7923 (ttp80) REVERT: A 561 GLN cc_start: 0.7762 (pt0) cc_final: 0.7501 (tt0) REVERT: C 53 ARG cc_start: 0.8319 (ttm170) cc_final: 0.7785 (ttp80) REVERT: C 356 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7291 (m-30) REVERT: C 589 SER cc_start: 0.8116 (t) cc_final: 0.7606 (m) REVERT: B 32 PHE cc_start: 0.7913 (t80) cc_final: 0.7617 (t80) REVERT: B 53 ARG cc_start: 0.8342 (ttm170) cc_final: 0.7757 (ttp80) REVERT: B 356 ASP cc_start: 0.7500 (t70) cc_final: 0.7255 (m-30) REVERT: B 589 SER cc_start: 0.8127 (t) cc_final: 0.7606 (m) outliers start: 31 outliers final: 20 residues processed: 177 average time/residue: 1.2683 time to fit residues: 246.4160 Evaluate side-chains 174 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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: 1.9990 chunk 41 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 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: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.173387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119388 restraints weight = 34146.225| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.72 r_work: 0.3278 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14451 Z= 0.211 Angle : 0.622 6.716 19536 Z= 0.306 Chirality : 0.046 0.378 2118 Planarity : 0.005 0.041 2391 Dihedral : 9.748 152.377 2821 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.38 % Allowed : 15.61 % Favored : 82.01 % 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: 0.11 (0.21), residues: 1620 helix: 1.00 (0.25), residues: 444 sheet: -0.46 (0.24), residues: 420 loop : -0.01 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 264 TYR 0.013 0.002 TYR C 40 PHE 0.018 0.002 PHE A 275 TRP 0.009 0.002 TRP B 575 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00486 (14376) covalent geometry : angle 0.58496 (19422) SS BOND : bond 0.00476 ( 12) SS BOND : angle 1.91729 ( 24) hydrogen bonds : bond 0.04494 ( 572) hydrogen bonds : angle 5.84711 ( 1644) metal coordination : bond 0.00630 ( 24) metal coordination : angle 3.89540 ( 36) Misc. bond : bond 0.00046 ( 21) link_BETA1-4 : bond 0.00521 ( 6) link_BETA1-4 : angle 1.83365 ( 18) link_NAG-ASN : bond 0.00611 ( 12) link_NAG-ASN : angle 2.38906 ( 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 196 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8490 (ttm170) cc_final: 0.7995 (ttp80) REVERT: A 521 HIS cc_start: 0.7478 (m-70) cc_final: 0.7181 (m90) REVERT: A 551 ARG cc_start: 0.7569 (mmt90) cc_final: 0.7061 (mtm110) REVERT: A 589 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7427 (m) REVERT: C 53 ARG cc_start: 0.8457 (ttm170) cc_final: 0.7867 (ttp80) REVERT: C 551 ARG cc_start: 0.7524 (mmt90) cc_final: 0.7177 (mtp-110) REVERT: C 589 SER cc_start: 0.8185 (t) cc_final: 0.7681 (m) REVERT: B 32 PHE cc_start: 0.7960 (t80) cc_final: 0.7626 (t80) REVERT: B 53 ARG cc_start: 0.8482 (ttm170) cc_final: 0.7873 (ttp80) REVERT: B 295 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.8463 (t80) REVERT: B 521 HIS cc_start: 0.7140 (m-70) cc_final: 0.6726 (m90) REVERT: B 551 ARG cc_start: 0.7609 (mmt90) cc_final: 0.7256 (mtp-110) REVERT: B 589 SER cc_start: 0.8120 (t) cc_final: 0.7603 (m) outliers start: 35 outliers final: 24 residues processed: 185 average time/residue: 1.4548 time to fit residues: 292.8194 Evaluate side-chains 182 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 295 TYR 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: 1.9990 chunk 123 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.174044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120527 restraints weight = 34088.222| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.72 r_work: 0.3296 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14451 Z= 0.156 Angle : 0.569 6.854 19536 Z= 0.279 Chirality : 0.045 0.374 2118 Planarity : 0.004 0.044 2391 Dihedral : 9.208 146.130 2821 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.17 % Allowed : 16.63 % 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: 0.22 (0.21), residues: 1620 helix: 1.15 (0.25), residues: 444 sheet: -0.51 (0.24), residues: 420 loop : 0.09 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 236 TYR 0.011 0.001 TYR C 40 PHE 0.012 0.001 PHE C 275 TRP 0.009 0.001 TRP B 575 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00351 (14376) covalent geometry : angle 0.53567 (19422) SS BOND : bond 0.00522 ( 12) SS BOND : angle 1.77732 ( 24) hydrogen bonds : bond 0.03885 ( 572) hydrogen bonds : angle 5.62294 ( 1644) metal coordination : bond 0.00513 ( 24) metal coordination : angle 3.74321 ( 36) Misc. bond : bond 0.00028 ( 21) link_BETA1-4 : bond 0.00073 ( 6) link_BETA1-4 : angle 1.53840 ( 18) link_NAG-ASN : bond 0.00352 ( 12) link_NAG-ASN : angle 1.97013 ( 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 188 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8479 (ttm170) cc_final: 0.7973 (ttp80) REVERT: A 217 THR cc_start: 0.8520 (m) cc_final: 0.8274 (t) REVERT: A 521 HIS cc_start: 0.7447 (m-70) cc_final: 0.7114 (m90) REVERT: A 551 ARG cc_start: 0.7610 (mmt90) cc_final: 0.7178 (mtm110) REVERT: A 589 SER cc_start: 0.8140 (t) cc_final: 0.7441 (m) REVERT: C 53 ARG cc_start: 0.8437 (ttm170) cc_final: 0.7775 (ttp80) REVERT: C 551 ARG cc_start: 0.7534 (mmt90) cc_final: 0.7026 (mtm110) REVERT: C 589 SER cc_start: 0.8159 (t) cc_final: 0.7700 (m) REVERT: B 32 PHE cc_start: 0.7947 (t80) cc_final: 0.7615 (t80) REVERT: B 53 ARG cc_start: 0.8473 (ttm170) cc_final: 0.7879 (ttp80) REVERT: B 521 HIS cc_start: 0.7184 (m-70) cc_final: 0.6785 (m90) REVERT: B 551 ARG cc_start: 0.7626 (mmt90) cc_final: 0.7178 (mtm110) REVERT: B 589 SER cc_start: 0.8107 (t) cc_final: 0.7613 (m) outliers start: 32 outliers final: 27 residues processed: 178 average time/residue: 1.4157 time to fit residues: 275.1951 Evaluate side-chains 182 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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 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 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 264 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.172857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.118819 restraints weight = 33926.402| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.73 r_work: 0.3284 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14451 Z= 0.185 Angle : 0.585 6.906 19536 Z= 0.286 Chirality : 0.045 0.379 2118 Planarity : 0.004 0.043 2391 Dihedral : 9.068 138.138 2821 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.38 % Allowed : 16.50 % 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: 0.27 (0.21), residues: 1620 helix: 1.17 (0.25), residues: 444 sheet: -0.46 (0.24), residues: 420 loop : 0.13 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 276 TYR 0.014 0.002 TYR B 295 PHE 0.014 0.002 PHE A 275 TRP 0.009 0.001 TRP B 575 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00425 (14376) covalent geometry : angle 0.54984 (19422) SS BOND : bond 0.00447 ( 12) SS BOND : angle 1.82795 ( 24) hydrogen bonds : bond 0.03949 ( 572) hydrogen bonds : angle 5.52410 ( 1644) metal coordination : bond 0.00577 ( 24) metal coordination : angle 3.75593 ( 36) Misc. bond : bond 0.00026 ( 21) link_BETA1-4 : bond 0.00193 ( 6) link_BETA1-4 : angle 1.86268 ( 18) link_NAG-ASN : bond 0.00429 ( 12) link_NAG-ASN : angle 2.16198 ( 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 196 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.712 Fit side-chains REVERT: A 53 ARG cc_start: 0.8499 (ttm170) cc_final: 0.7968 (ttp80) REVERT: A 512 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8101 (mp) REVERT: A 521 HIS cc_start: 0.7476 (m-70) cc_final: 0.7157 (m90) REVERT: A 551 ARG cc_start: 0.7621 (mmt90) cc_final: 0.7223 (mtm110) REVERT: A 589 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7412 (m) REVERT: C 53 ARG cc_start: 0.8495 (ttm170) cc_final: 0.7906 (ttp80) REVERT: C 551 ARG cc_start: 0.7535 (mmt90) cc_final: 0.7067 (mtm110) REVERT: C 589 SER cc_start: 0.8141 (t) cc_final: 0.7706 (m) REVERT: B 32 PHE cc_start: 0.7971 (t80) cc_final: 0.7646 (t80) REVERT: B 53 ARG cc_start: 0.8486 (ttm170) cc_final: 0.7834 (ttp80) REVERT: B 521 HIS cc_start: 0.7186 (m-70) cc_final: 0.6792 (m90) REVERT: B 551 ARG cc_start: 0.7700 (mmt90) cc_final: 0.7270 (mtm110) REVERT: B 589 SER cc_start: 0.8100 (t) cc_final: 0.7620 (m) outliers start: 35 outliers final: 27 residues processed: 184 average time/residue: 1.3410 time to fit residues: 269.1883 Evaluate side-chains 186 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 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 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 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 366 HIS 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: 0.1980 chunk 90 optimal weight: 0.0570 chunk 59 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.174202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120687 restraints weight = 34017.180| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.73 r_work: 0.3309 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14451 Z= 0.122 Angle : 0.538 6.839 19536 Z= 0.262 Chirality : 0.044 0.376 2118 Planarity : 0.004 0.043 2391 Dihedral : 8.451 125.005 2820 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.38 % Allowed : 16.43 % 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: 0.42 (0.21), residues: 1620 helix: 1.51 (0.25), residues: 441 sheet: -0.53 (0.24), residues: 420 loop : 0.18 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 546 TYR 0.010 0.001 TYR C 40 PHE 0.010 0.001 PHE A 275 TRP 0.009 0.001 TRP B 575 HIS 0.001 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00273 (14376) covalent geometry : angle 0.50695 (19422) SS BOND : bond 0.00459 ( 12) SS BOND : angle 1.66262 ( 24) hydrogen bonds : bond 0.03446 ( 572) hydrogen bonds : angle 5.30239 ( 1644) metal coordination : bond 0.00469 ( 24) metal coordination : angle 3.52357 ( 36) Misc. bond : bond 0.00015 ( 21) link_BETA1-4 : bond 0.00070 ( 6) link_BETA1-4 : angle 1.46574 ( 18) link_NAG-ASN : bond 0.00252 ( 12) link_NAG-ASN : angle 1.77523 ( 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: 35 poor density : 160 time to evaluate : 0.747 Fit side-chains REVERT: A 24 MET cc_start: 0.8164 (mmp) cc_final: 0.7871 (mmm) REVERT: A 53 ARG cc_start: 0.8480 (ttm170) cc_final: 0.7961 (ttp80) REVERT: A 217 THR cc_start: 0.8442 (m) cc_final: 0.8224 (t) REVERT: A 512 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 521 HIS cc_start: 0.7429 (m-70) cc_final: 0.7115 (m90) REVERT: A 551 ARG cc_start: 0.7594 (mmt90) cc_final: 0.7199 (mtm110) REVERT: A 589 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7435 (m) REVERT: C 53 ARG cc_start: 0.8467 (ttm170) cc_final: 0.7869 (ttp80) REVERT: C 486 GLN cc_start: 0.6784 (OUTLIER) cc_final: 0.6517 (mt0) REVERT: C 551 ARG cc_start: 0.7486 (mmt90) cc_final: 0.7052 (mtm110) REVERT: C 589 SER cc_start: 0.8091 (t) cc_final: 0.7693 (m) REVERT: B 32 PHE cc_start: 0.7949 (t80) cc_final: 0.7634 (t80) REVERT: B 53 ARG cc_start: 0.8443 (ttm170) cc_final: 0.7818 (ttp80) REVERT: B 521 HIS cc_start: 0.7174 (m-70) cc_final: 0.6792 (m90) REVERT: B 551 ARG cc_start: 0.7697 (mmt90) cc_final: 0.7252 (mtm110) REVERT: B 589 SER cc_start: 0.8041 (t) cc_final: 0.7597 (m) outliers start: 35 outliers final: 23 residues processed: 182 average time/residue: 1.3611 time to fit residues: 270.4694 Evaluate side-chains 185 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 356 ASP 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 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 486 GLN 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 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: 0.9980 chunk 96 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.172113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117907 restraints weight = 33783.129| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.73 r_work: 0.3279 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14451 Z= 0.198 Angle : 0.594 6.794 19536 Z= 0.289 Chirality : 0.045 0.381 2118 Planarity : 0.004 0.041 2391 Dihedral : 8.697 117.371 2818 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.10 % Allowed : 16.36 % Favored : 81.53 % 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: 0.39 (0.21), residues: 1620 helix: 1.42 (0.25), residues: 441 sheet: -0.49 (0.24), residues: 420 loop : 0.16 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.014 0.002 TYR B 295 PHE 0.016 0.002 PHE A 235 TRP 0.009 0.001 TRP B 575 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00453 (14376) covalent geometry : angle 0.55776 (19422) SS BOND : bond 0.00431 ( 12) SS BOND : angle 1.88648 ( 24) hydrogen bonds : bond 0.03943 ( 572) hydrogen bonds : angle 5.47985 ( 1644) metal coordination : bond 0.00606 ( 24) metal coordination : angle 3.78456 ( 36) Misc. bond : bond 0.00038 ( 21) link_BETA1-4 : bond 0.00214 ( 6) link_BETA1-4 : angle 1.98953 ( 18) link_NAG-ASN : bond 0.00482 ( 12) link_NAG-ASN : angle 2.22154 ( 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 191 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.776 Fit side-chains REVERT: A 53 ARG cc_start: 0.8506 (ttm170) cc_final: 0.7945 (ttp80) REVERT: A 217 THR cc_start: 0.8642 (m) cc_final: 0.8369 (t) REVERT: A 512 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8123 (mp) REVERT: A 521 HIS cc_start: 0.7485 (m-70) cc_final: 0.7179 (m90) REVERT: A 551 ARG cc_start: 0.7609 (mmt90) cc_final: 0.7234 (mtm110) REVERT: A 562 ASP cc_start: 0.8069 (m-30) cc_final: 0.7628 (m-30) REVERT: A 589 SER cc_start: 0.7962 (OUTLIER) cc_final: 0.7389 (m) REVERT: C 53 ARG cc_start: 0.8504 (ttm170) cc_final: 0.7913 (ttp80) REVERT: C 551 ARG cc_start: 0.7544 (mmt90) cc_final: 0.7154 (mtm110) REVERT: C 589 SER cc_start: 0.8076 (t) cc_final: 0.7693 (m) REVERT: B 32 PHE cc_start: 0.7954 (t80) cc_final: 0.7653 (t80) REVERT: B 53 ARG cc_start: 0.8454 (ttm170) cc_final: 0.7916 (ttp80) REVERT: B 521 HIS cc_start: 0.7188 (m-70) cc_final: 0.6820 (m90) REVERT: B 551 ARG cc_start: 0.7706 (mmt90) cc_final: 0.7290 (mtm110) REVERT: B 589 SER cc_start: 0.8036 (t) cc_final: 0.7590 (m) outliers start: 31 outliers final: 22 residues processed: 180 average time/residue: 1.2490 time to fit residues: 246.0473 Evaluate side-chains 180 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 356 ASP 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 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 36 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 189 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: 1.9990 chunk 48 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.172303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.118169 restraints weight = 33859.194| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.73 r_work: 0.3274 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14451 Z= 0.203 Angle : 0.595 6.933 19536 Z= 0.291 Chirality : 0.045 0.382 2118 Planarity : 0.004 0.046 2391 Dihedral : 8.609 102.014 2818 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.97 % Allowed : 16.90 % 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: 0.32 (0.21), residues: 1620 helix: 1.15 (0.25), residues: 462 sheet: -0.47 (0.25), residues: 420 loop : 0.20 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.013 0.002 TYR C 40 PHE 0.016 0.002 PHE C 102 TRP 0.009 0.002 TRP A 31 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00465 (14376) covalent geometry : angle 0.55907 (19422) SS BOND : bond 0.00475 ( 12) SS BOND : angle 1.87408 ( 24) hydrogen bonds : bond 0.03906 ( 572) hydrogen bonds : angle 5.47366 ( 1644) metal coordination : bond 0.00629 ( 24) metal coordination : angle 3.82258 ( 36) Misc. bond : bond 0.00037 ( 21) link_BETA1-4 : bond 0.00163 ( 6) link_BETA1-4 : angle 1.83755 ( 18) link_NAG-ASN : bond 0.00470 ( 12) link_NAG-ASN : angle 2.18376 ( 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: 29 poor density : 156 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.8166 (mmp) cc_final: 0.7865 (mmm) REVERT: A 53 ARG cc_start: 0.8509 (ttm170) cc_final: 0.7946 (ttp80) REVERT: A 217 THR cc_start: 0.8640 (m) cc_final: 0.8374 (t) REVERT: A 512 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8092 (mp) REVERT: A 521 HIS cc_start: 0.7495 (m-70) cc_final: 0.7204 (m90) REVERT: A 551 ARG cc_start: 0.7613 (mmt90) cc_final: 0.7236 (mtm110) REVERT: A 589 SER cc_start: 0.7904 (OUTLIER) cc_final: 0.7355 (m) REVERT: C 53 ARG cc_start: 0.8489 (ttm170) cc_final: 0.7905 (ttp80) REVERT: C 521 HIS cc_start: 0.7124 (m-70) cc_final: 0.6773 (m90) REVERT: C 551 ARG cc_start: 0.7525 (mmt90) cc_final: 0.7158 (mtm110) REVERT: C 589 SER cc_start: 0.8009 (t) cc_final: 0.7618 (m) REVERT: B 32 PHE cc_start: 0.7972 (t80) cc_final: 0.7680 (t80) REVERT: B 53 ARG cc_start: 0.8460 (ttm170) cc_final: 0.7915 (ttp80) REVERT: B 521 HIS cc_start: 0.7158 (m-70) cc_final: 0.6819 (m90) REVERT: B 551 ARG cc_start: 0.7695 (mmt90) cc_final: 0.7285 (mtm110) REVERT: B 589 SER cc_start: 0.7993 (t) cc_final: 0.7544 (m) outliers start: 29 outliers final: 23 residues processed: 173 average time/residue: 1.3094 time to fit residues: 248.3363 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 : 0.687 ------------------------------------------------------------------------------- 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 362 CYS Chi-restraints excluded: chain C residue 363 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 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: 1.9990 chunk 83 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 120 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120047 restraints weight = 33911.690| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.74 r_work: 0.3307 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14451 Z= 0.122 Angle : 0.538 6.987 19536 Z= 0.262 Chirality : 0.044 0.379 2118 Planarity : 0.004 0.042 2391 Dihedral : 7.913 77.751 2818 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.70 % Allowed : 17.24 % Favored : 81.06 % 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: 1.42 (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 0.005 0.000 ARG A 236 TYR 0.013 0.001 TYR B 295 PHE 0.011 0.001 PHE C 32 TRP 0.009 0.001 TRP B 575 HIS 0.002 0.000 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00277 (14376) covalent geometry : angle 0.50534 (19422) SS BOND : bond 0.00437 ( 12) SS BOND : angle 1.64159 ( 24) hydrogen bonds : bond 0.03408 ( 572) hydrogen bonds : angle 5.24388 ( 1644) metal coordination : bond 0.00493 ( 24) metal coordination : angle 3.59057 ( 36) Misc. bond : bond 0.00016 ( 21) link_BETA1-4 : bond 0.00121 ( 6) link_BETA1-4 : angle 1.58492 ( 18) link_NAG-ASN : bond 0.00242 ( 12) link_NAG-ASN : angle 1.77851 ( 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 186 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8490 (ttm170) cc_final: 0.7954 (ttp80) REVERT: A 72 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7468 (mttp) REVERT: A 217 THR cc_start: 0.8437 (m) cc_final: 0.8227 (t) REVERT: A 512 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8069 (mp) REVERT: A 521 HIS cc_start: 0.7454 (m-70) cc_final: 0.7157 (m90) REVERT: A 551 ARG cc_start: 0.7584 (mmt90) cc_final: 0.7222 (mtm110) REVERT: A 589 SER cc_start: 0.7886 (t) cc_final: 0.7337 (m) REVERT: C 53 ARG cc_start: 0.8482 (ttm170) cc_final: 0.7907 (ttp80) REVERT: C 521 HIS cc_start: 0.7088 (m-70) cc_final: 0.6742 (m90) REVERT: C 551 ARG cc_start: 0.7518 (mmt90) cc_final: 0.7121 (mtm110) REVERT: C 589 SER cc_start: 0.8046 (t) cc_final: 0.7656 (m) REVERT: B 32 PHE cc_start: 0.7928 (t80) cc_final: 0.7646 (t80) REVERT: B 53 ARG cc_start: 0.8437 (ttm170) cc_final: 0.7915 (ttp80) REVERT: B 521 HIS cc_start: 0.7126 (m-70) cc_final: 0.6795 (m90) REVERT: B 551 ARG cc_start: 0.7651 (mmt90) cc_final: 0.7239 (mtm110) REVERT: B 589 SER cc_start: 0.7972 (t) cc_final: 0.7525 (m) outliers start: 25 outliers final: 20 residues processed: 178 average time/residue: 1.2867 time to fit residues: 250.8491 Evaluate side-chains 179 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 72 LYS 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 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 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: 0.5980 chunk 13 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.173335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119155 restraints weight = 33553.280| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.74 r_work: 0.3284 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2646 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= 0.149 Angle : 0.552 6.617 19536 Z= 0.269 Chirality : 0.044 0.381 2118 Planarity : 0.004 0.041 2391 Dihedral : 7.874 65.166 2818 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.49 % Allowed : 17.52 % 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: 0.47 (0.21), residues: 1620 helix: 1.43 (0.25), residues: 462 sheet: -0.55 (0.24), residues: 420 loop : 0.30 (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 0.012 0.001 PHE A 275 TRP 0.009 0.001 TRP B 575 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00340 (14376) covalent geometry : angle 0.51821 (19422) SS BOND : bond 0.00434 ( 12) SS BOND : angle 1.74604 ( 24) hydrogen bonds : bond 0.03549 ( 572) hydrogen bonds : angle 5.25779 ( 1644) metal coordination : bond 0.00519 ( 24) metal coordination : angle 3.61366 ( 36) Misc. bond : bond 0.00023 ( 21) link_BETA1-4 : bond 0.00069 ( 6) link_BETA1-4 : angle 1.74312 ( 18) link_NAG-ASN : bond 0.00335 ( 12) link_NAG-ASN : angle 1.92415 ( 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 182 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.683 Fit side-chains REVERT: A 53 ARG cc_start: 0.8501 (ttm170) cc_final: 0.7964 (ttp80) REVERT: A 72 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7465 (mttp) REVERT: A 217 THR cc_start: 0.8501 (m) cc_final: 0.8281 (t) REVERT: A 512 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8110 (mp) REVERT: A 521 HIS cc_start: 0.7446 (m-70) cc_final: 0.7155 (m90) REVERT: A 551 ARG cc_start: 0.7620 (mmt90) cc_final: 0.7215 (mtm110) REVERT: A 589 SER cc_start: 0.7919 (t) cc_final: 0.7364 (m) REVERT: C 53 ARG cc_start: 0.8480 (ttm170) cc_final: 0.7899 (ttp80) REVERT: C 521 HIS cc_start: 0.7058 (m-70) cc_final: 0.6723 (m90) REVERT: C 551 ARG cc_start: 0.7585 (mmt90) cc_final: 0.7173 (mtm110) REVERT: C 589 SER cc_start: 0.8081 (t) cc_final: 0.7672 (m) REVERT: B 32 PHE cc_start: 0.7914 (t80) cc_final: 0.7641 (t80) REVERT: B 53 ARG cc_start: 0.8460 (ttm170) cc_final: 0.7912 (ttp80) REVERT: B 521 HIS cc_start: 0.7116 (m-70) cc_final: 0.6794 (m90) REVERT: B 551 ARG cc_start: 0.7673 (mmt90) cc_final: 0.7251 (mtm110) REVERT: B 589 SER cc_start: 0.7990 (t) cc_final: 0.7529 (m) outliers start: 22 outliers final: 20 residues processed: 176 average time/residue: 1.3949 time to fit residues: 268.5234 Evaluate side-chains 181 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 72 LYS 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 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 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: 0.8980 chunk 152 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 144 optimal weight: 0.3980 chunk 153 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119970 restraints weight = 33466.835| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.71 r_work: 0.3291 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2682 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= 0.136 Angle : 0.542 6.669 19536 Z= 0.264 Chirality : 0.044 0.380 2118 Planarity : 0.004 0.041 2391 Dihedral : 7.762 60.434 2818 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.56 % Allowed : 17.38 % Favored : 81.06 % 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: 0.51 (0.21), residues: 1620 helix: 1.49 (0.25), residues: 462 sheet: -0.54 (0.24), residues: 420 loop : 0.32 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.010 0.001 TYR B 40 PHE 0.010 0.001 PHE A 235 TRP 0.009 0.001 TRP B 575 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00307 (14376) covalent geometry : angle 0.50967 (19422) SS BOND : bond 0.00446 ( 12) SS BOND : angle 1.70418 ( 24) hydrogen bonds : bond 0.03451 ( 572) hydrogen bonds : angle 5.21319 ( 1644) metal coordination : bond 0.00500 ( 24) metal coordination : angle 3.56850 ( 36) Misc. bond : bond 0.00020 ( 21) link_BETA1-4 : bond 0.00127 ( 6) link_BETA1-4 : angle 1.62423 ( 18) link_NAG-ASN : bond 0.00293 ( 12) link_NAG-ASN : angle 1.83945 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10690.64 seconds wall clock time: 181 minutes 26.04 seconds (10886.04 seconds total)