Starting phenix.real_space_refine on Sat Jul 4 20:51:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x6c_33021/07_2026/7x6c_33021.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x6c_33021/07_2026/7x6c_33021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x6c_33021/07_2026/7x6c_33021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x6c_33021/07_2026/7x6c_33021.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7x6c_33021/07_2026/7x6c_33021.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x6c_33021/07_2026/7x6c_33021.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x6c_33021/07_2026/7x6c_33021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x6c_33021/07_2026/7x6c_33021.map" } resolution = 3.15 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= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 116 5.16 5 C 14840 2.51 5 N 3640 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22632 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5501 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Chain: "A" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5501 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Chain: "B" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5501 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Chain: "D" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5501 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS C 176 62.296 98.972 74.070 1.00 72.21 S ATOM 1162 SG CYS C 178 64.600 101.780 75.305 1.00 73.13 S ATOM 1184 SG CYS C 181 65.020 98.311 76.766 1.00 63.41 S ATOM 6649 SG CYS A 176 50.627 13.965 74.119 1.00 72.01 S ATOM 6663 SG CYS A 178 48.324 11.158 75.358 1.00 72.83 S ATOM 6685 SG CYS A 181 47.902 14.627 76.815 1.00 63.43 S ATOM 12150 SG CYS B 176 99.061 50.536 74.100 1.00 71.76 S ATOM 12164 SG CYS B 178 101.869 48.233 75.337 1.00 72.76 S ATOM 12186 SG CYS B 181 98.400 47.812 76.796 1.00 61.99 S ATOM 17651 SG CYS D 176 13.838 62.396 74.082 1.00 71.38 S ATOM 17665 SG CYS D 178 11.029 64.699 75.316 1.00 72.17 S ATOM 17687 SG CYS D 181 14.497 65.123 76.776 1.00 62.05 S Time building chain proxies: 5.09, per 1000 atoms: 0.22 Number of scatterers: 22632 At special positions: 0 Unit cell: (114.03, 114.03, 137.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 116 16.00 P 8 15.00 O 4020 8.00 N 3640 7.00 C 14840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 176 " pdb=" ZN B 805 " pdb="ZN ZN B 805 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 176 " pdb=" ZN C 804 " pdb="ZN ZN C 804 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 176 " pdb=" ZN D 805 " pdb="ZN ZN D 805 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 176 " Number of angles added : 12 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5200 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 74.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.581A pdb=" N PHE C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.614A pdb=" N MET C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 107 Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.593A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 178 through 188 removed outlier: 3.906A pdb=" N SER C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 215 through 234 removed outlier: 3.857A pdb=" N LYS C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 257 removed outlier: 3.789A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 401 through 424 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 465 through 469 removed outlier: 3.562A pdb=" N TRP C 469 " --> pdb=" O ARG C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 499 removed outlier: 4.130A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 3.936A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 549 through 553 removed outlier: 3.510A pdb=" N ASN C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.824A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 588 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 614 Processing helix chain 'C' and resid 615 through 632 Processing helix chain 'C' and resid 635 through 649 removed outlier: 3.728A pdb=" N TRP C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 732 Processing helix chain 'C' and resid 734 through 758 Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.581A pdb=" N PHE A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.615A pdb=" N MET A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.593A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.907A pdb=" N SER A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.856A pdb=" N LYS A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 257 removed outlier: 3.789A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 401 through 424 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.562A pdb=" N TRP A 469 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 499 removed outlier: 4.129A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 3.935A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.511A pdb=" N ASN A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.823A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 588 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'A' and resid 615 through 632 Processing helix chain 'A' and resid 635 through 649 removed outlier: 3.729A pdb=" N TRP A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 732 Processing helix chain 'A' and resid 734 through 758 Processing helix chain 'B' and resid 30 through 43 removed outlier: 3.582A pdb=" N PHE B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.615A pdb=" N MET B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.593A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 178 through 188 removed outlier: 3.906A pdb=" N SER B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 215 through 234 removed outlier: 3.855A pdb=" N LYS B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 257 removed outlier: 3.788A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 362 through 384 Processing helix chain 'B' and resid 401 through 424 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.562A pdb=" N TRP B 469 " --> pdb=" O ARG B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 499 removed outlier: 4.130A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 3.936A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 549 through 553 removed outlier: 3.511A pdb=" N ASN B 552 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.824A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 588 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 614 Processing helix chain 'B' and resid 615 through 632 Processing helix chain 'B' and resid 635 through 649 removed outlier: 3.729A pdb=" N TRP B 639 " --> pdb=" O ALA B 635 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 732 Processing helix chain 'B' and resid 734 through 758 Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.582A pdb=" N PHE D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 58 Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.614A pdb=" N MET D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 107 Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.594A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 178 through 188 removed outlier: 3.906A pdb=" N SER D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.855A pdb=" N LYS D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 257 removed outlier: 3.788A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 362 through 384 Processing helix chain 'D' and resid 401 through 424 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.563A pdb=" N TRP D 469 " --> pdb=" O ARG D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 499 removed outlier: 4.130A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 3.935A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D 519 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.511A pdb=" N ASN D 552 " --> pdb=" O GLU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.824A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 588 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 614 Processing helix chain 'D' and resid 615 through 632 Processing helix chain 'D' and resid 635 through 649 removed outlier: 3.729A pdb=" N TRP D 639 " --> pdb=" O ALA D 635 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 649 " --> pdb=" O LYS D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 732 Processing helix chain 'D' and resid 734 through 758 Processing sheet with id=AA1, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'C' and resid 167 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 168 1384 hydrogen bonds defined for protein. 4068 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: 4.28 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3568 1.32 - 1.44: 6208 1.44 - 1.56: 13168 1.56 - 1.69: 20 1.69 - 1.81: 188 Bond restraints: 23152 Sorted by residual: bond pdb=" O12 POV C 802 " pdb=" P POV C 802 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" O12 POV D 803 " pdb=" P POV D 803 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" O12 POV B 803 " pdb=" P POV B 803 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" O12 POV A 802 " pdb=" P POV A 802 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" C1 POV B 803 " pdb=" O11 POV B 803 " ideal model delta sigma weight residual 1.410 1.459 -0.049 2.00e-02 2.50e+03 5.95e+00 ... (remaining 23147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 30702 2.29 - 4.57: 495 4.57 - 6.86: 83 6.86 - 9.14: 12 9.14 - 11.43: 16 Bond angle restraints: 31308 Sorted by residual: angle pdb=" C ILE D 729 " pdb=" N ARG D 730 " pdb=" CA ARG D 730 " ideal model delta sigma weight residual 122.26 112.04 10.22 1.73e+00 3.34e-01 3.49e+01 angle pdb=" C ILE A 729 " pdb=" N ARG A 730 " pdb=" CA ARG A 730 " ideal model delta sigma weight residual 122.26 112.08 10.18 1.73e+00 3.34e-01 3.46e+01 angle pdb=" C ILE B 729 " pdb=" N ARG B 730 " pdb=" CA ARG B 730 " ideal model delta sigma weight residual 122.26 112.08 10.18 1.73e+00 3.34e-01 3.46e+01 angle pdb=" C ILE C 729 " pdb=" N ARG C 730 " pdb=" CA ARG C 730 " ideal model delta sigma weight residual 122.26 112.10 10.16 1.73e+00 3.34e-01 3.45e+01 angle pdb=" CA GLU B 81 " pdb=" CB GLU B 81 " pdb=" CG GLU B 81 " ideal model delta sigma weight residual 114.10 125.53 -11.43 2.00e+00 2.50e-01 3.26e+01 ... (remaining 31303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 13464 35.59 - 71.19: 317 71.19 - 106.78: 23 106.78 - 142.38: 20 142.38 - 177.97: 4 Dihedral angle restraints: 13828 sinusoidal: 5832 harmonic: 7996 Sorted by residual: dihedral pdb=" C26 YZY D 801 " pdb=" C27 YZY D 801 " pdb=" C28 YZY D 801 " pdb=" C29 YZY D 801 " ideal model delta sinusoidal sigma weight residual 119.11 -58.86 177.97 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 806 " pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sinusoidal sigma weight residual 119.11 -58.84 177.95 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY B 801 " pdb=" C27 YZY B 801 " pdb=" C28 YZY B 801 " pdb=" C29 YZY B 801 " ideal model delta sinusoidal sigma weight residual 119.11 -58.81 177.92 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2586 0.044 - 0.088: 749 0.088 - 0.131: 137 0.131 - 0.175: 12 0.175 - 0.219: 12 Chirality restraints: 3496 Sorted by residual: chirality pdb=" CB VAL A 96 " pdb=" CA VAL A 96 " pdb=" CG1 VAL A 96 " pdb=" CG2 VAL A 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL D 96 " pdb=" CA VAL D 96 " pdb=" CG1 VAL D 96 " pdb=" CG2 VAL D 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL C 96 " pdb=" CA VAL C 96 " pdb=" CG1 VAL C 96 " pdb=" CG2 VAL C 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 3493 not shown) Planarity restraints: 3860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 YZY A 806 " 0.058 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C28 YZY A 806 " -0.059 2.00e-02 2.50e+03 pdb=" C29 YZY A 806 " -0.057 2.00e-02 2.50e+03 pdb=" C30 YZY A 806 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY D 801 " 0.058 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C28 YZY D 801 " -0.059 2.00e-02 2.50e+03 pdb=" C29 YZY D 801 " -0.057 2.00e-02 2.50e+03 pdb=" C30 YZY D 801 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY B 801 " 0.058 2.00e-02 2.50e+03 5.80e-02 3.37e+01 pdb=" C28 YZY B 801 " -0.059 2.00e-02 2.50e+03 pdb=" C29 YZY B 801 " -0.057 2.00e-02 2.50e+03 pdb=" C30 YZY B 801 " 0.058 2.00e-02 2.50e+03 ... (remaining 3857 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4577 2.78 - 3.31: 20921 3.31 - 3.84: 36619 3.84 - 4.37: 42157 4.37 - 4.90: 76147 Nonbonded interactions: 180421 Sorted by model distance: nonbonded pdb=" O HIS D 735 " pdb=" OG1 THR D 739 " model vdw 2.249 3.040 nonbonded pdb=" O HIS B 735 " pdb=" OG1 THR B 739 " model vdw 2.249 3.040 nonbonded pdb=" O HIS C 735 " pdb=" OG1 THR C 739 " model vdw 2.250 3.040 nonbonded pdb=" O HIS A 735 " pdb=" OG1 THR A 739 " model vdw 2.250 3.040 nonbonded pdb=" O ILE C 209 " pdb=" OG SER C 213 " model vdw 2.258 3.040 ... (remaining 180416 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 758) selection = (chain 'B' and resid 17 through 758) selection = (chain 'C' and resid 17 through 758) selection = (chain 'D' and resid 17 through 758) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 24.130 Find NCS groups from input model: 0.580 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: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.004 0.066 23172 Z= 0.210 Angle : 0.736 11.426 31328 Z= 0.383 Chirality : 0.042 0.219 3496 Planarity : 0.006 0.067 3860 Dihedral : 16.787 177.972 8616 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.66 % Allowed : 1.00 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 2668 helix: 0.34 (0.11), residues: 1884 sheet: None (None), residues: 0 loop : -1.33 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 730 TYR 0.025 0.001 TYR B 541 PHE 0.030 0.002 PHE D 743 TRP 0.015 0.001 TRP C 410 HIS 0.003 0.000 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (23152) covalent geometry : angle 0.73522 / 0.38 (31308) SS BOND : bond 0.00027 / 0.01 ( 4) SS BOND : angle 0.20892 / 0.15 ( 8) hydrogen bonds : bond 0.13342 / 9.08 ( 1384) hydrogen bonds : angle 4.86465 / 3.44 ( 4068) metal coordination : bond 0.01145 / 1.08 ( 16) metal coordination : angle 1.83889 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 312 time to evaluate : 0.988 Fit side-chains REVERT: C 551 ASN cc_start: 0.7513 (t0) cc_final: 0.7167 (t0) REVERT: A 741 GLU cc_start: 0.7397 (tp30) cc_final: 0.6985 (tp30) REVERT: B 516 ASP cc_start: 0.6720 (m-30) cc_final: 0.6291 (m-30) REVERT: D 516 ASP cc_start: 0.6773 (m-30) cc_final: 0.6333 (m-30) REVERT: D 631 ILE cc_start: 0.8157 (tp) cc_final: 0.7937 (tp) outliers start: 16 outliers final: 2 residues processed: 318 average time/residue: 0.1505 time to fit residues: 77.7895 Evaluate side-chains 265 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 263 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain A residue 648 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0770 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 625 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 432 HIS B 625 ASN D 163 GLN D 625 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.196873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151817 restraints weight = 22179.177| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.83 r_work: 0.3358 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 23172 Z= 0.117 Angle : 0.464 5.353 31328 Z= 0.247 Chirality : 0.036 0.136 3496 Planarity : 0.004 0.059 3860 Dihedral : 12.276 146.254 3302 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.66 % Allowed : 3.77 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.16), residues: 2668 helix: 1.46 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -0.93 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 730 TYR 0.014 0.001 TYR A 524 PHE 0.014 0.001 PHE A 743 TRP 0.013 0.001 TRP C 315 HIS 0.007 0.001 HIS C 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (23152) covalent geometry : angle 0.46243 / 0.25 (31308) SS BOND : bond 0.00083 / 0.04 ( 4) SS BOND : angle 0.41531 / 0.30 ( 8) hydrogen bonds : bond 0.03951 / 2.63 ( 1384) hydrogen bonds : angle 3.44163 / 2.45 ( 4068) metal coordination : bond 0.03205 / 3.80 ( 16) metal coordination : angle 1.81719 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 282 time to evaluate : 0.831 Fit side-chains REVERT: C 349 LEU cc_start: 0.8454 (mt) cc_final: 0.8184 (mt) REVERT: C 393 LEU cc_start: 0.8263 (mp) cc_final: 0.8024 (mt) REVERT: C 631 ILE cc_start: 0.8135 (tp) cc_final: 0.7710 (tp) REVERT: A 349 LEU cc_start: 0.8424 (mt) cc_final: 0.8115 (mt) REVERT: A 631 ILE cc_start: 0.8124 (tp) cc_final: 0.7724 (tp) REVERT: D 172 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6346 (t-90) REVERT: D 349 LEU cc_start: 0.8503 (mt) cc_final: 0.8184 (mt) REVERT: D 631 ILE cc_start: 0.8075 (tp) cc_final: 0.7748 (tp) outliers start: 16 outliers final: 7 residues processed: 292 average time/residue: 0.1466 time to fit residues: 70.0339 Evaluate side-chains 271 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 263 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 634 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 206 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 131 optimal weight: 0.0670 chunk 146 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 625 ASN C 629 GLN C 742 ASN A 629 GLN B 742 ASN D 163 GLN D 432 HIS D 625 ASN D 742 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.194989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151130 restraints weight = 22099.831| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.78 r_work: 0.3323 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23172 Z= 0.123 Angle : 0.457 5.739 31328 Z= 0.241 Chirality : 0.036 0.148 3496 Planarity : 0.004 0.043 3860 Dihedral : 10.585 146.520 3296 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.41 % Allowed : 5.43 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.16), residues: 2668 helix: 1.82 (0.12), residues: 1908 sheet: None (None), residues: 0 loop : -0.86 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 730 TYR 0.014 0.001 TYR A 524 PHE 0.021 0.001 PHE C 427 TRP 0.015 0.001 TRP A 315 HIS 0.007 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (23152) covalent geometry : angle 0.45427 / 0.24 (31308) SS BOND : bond 0.00039 / 0.02 ( 4) SS BOND : angle 0.15799 / 0.12 ( 8) hydrogen bonds : bond 0.03948 / 2.65 ( 1384) hydrogen bonds : angle 3.36343 / 2.39 ( 4068) metal coordination : bond 0.02577 / 2.95 ( 16) metal coordination : angle 2.38821 / 1.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 274 time to evaluate : 0.854 Fit side-chains REVERT: C 349 LEU cc_start: 0.8247 (mt) cc_final: 0.7974 (mt) REVERT: C 355 ASN cc_start: 0.7792 (t0) cc_final: 0.7557 (t0) REVERT: C 516 ASP cc_start: 0.7296 (m-30) cc_final: 0.7032 (m-30) REVERT: C 631 ILE cc_start: 0.8147 (tp) cc_final: 0.7732 (tp) REVERT: C 730 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7420 (ttt-90) REVERT: A 349 LEU cc_start: 0.8233 (mt) cc_final: 0.7973 (mt) REVERT: A 355 ASN cc_start: 0.7785 (t0) cc_final: 0.7564 (t0) REVERT: A 516 ASP cc_start: 0.7291 (m-30) cc_final: 0.7040 (m-30) REVERT: A 631 ILE cc_start: 0.8147 (tp) cc_final: 0.7795 (tp) REVERT: A 730 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7241 (ttt-90) REVERT: B 197 LEU cc_start: 0.8898 (tp) cc_final: 0.8644 (tp) REVERT: B 349 LEU cc_start: 0.8390 (mt) cc_final: 0.8168 (mt) REVERT: D 172 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6225 (t-90) REVERT: D 197 LEU cc_start: 0.8889 (tp) cc_final: 0.8641 (tp) REVERT: D 349 LEU cc_start: 0.8443 (mt) cc_final: 0.8128 (mt) REVERT: D 631 ILE cc_start: 0.8092 (tp) cc_final: 0.7785 (tp) outliers start: 10 outliers final: 9 residues processed: 279 average time/residue: 0.1457 time to fit residues: 66.8130 Evaluate side-chains 274 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 264 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 634 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 139 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 742 ASN A 742 ASN D 163 GLN D 742 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.189010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141706 restraints weight = 21860.343| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.98 r_work: 0.3236 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 23172 Z= 0.256 Angle : 0.596 6.068 31328 Z= 0.310 Chirality : 0.041 0.135 3496 Planarity : 0.004 0.045 3860 Dihedral : 10.645 146.654 3296 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.95 % Allowed : 8.00 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.16), residues: 2668 helix: 1.49 (0.12), residues: 1916 sheet: None (None), residues: 0 loop : -0.81 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 730 TYR 0.015 0.002 TYR B 524 PHE 0.017 0.002 PHE C 580 TRP 0.025 0.002 TRP C 315 HIS 0.007 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.26 (23152) covalent geometry : angle 0.59281 / 0.31 (31308) SS BOND : bond 0.00026 / 0.01 ( 4) SS BOND : angle 0.28772 / 0.17 ( 8) hydrogen bonds : bond 0.05400 / 3.61 ( 1384) hydrogen bonds : angle 3.56545 / 2.53 ( 4068) metal coordination : bond 0.02229 / 2.50 ( 16) metal coordination : angle 3.00301 / 1.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.922 Fit side-chains REVERT: C 393 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8160 (mt) REVERT: C 619 MET cc_start: 0.7994 (ttt) cc_final: 0.7720 (ttt) REVERT: C 631 ILE cc_start: 0.8212 (tp) cc_final: 0.7823 (tp) REVERT: A 619 MET cc_start: 0.8066 (ttt) cc_final: 0.7782 (ttt) REVERT: A 631 ILE cc_start: 0.8208 (tp) cc_final: 0.7832 (tp) REVERT: B 619 MET cc_start: 0.8087 (ttt) cc_final: 0.7842 (ttt) REVERT: B 657 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7927 (mm) REVERT: D 172 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6271 (t-90) REVERT: D 516 ASP cc_start: 0.7411 (m-30) cc_final: 0.7151 (m-30) REVERT: D 619 MET cc_start: 0.8085 (ttt) cc_final: 0.7838 (ttt) REVERT: D 631 ILE cc_start: 0.8213 (tp) cc_final: 0.7863 (tp) REVERT: D 715 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7295 (mp0) outliers start: 23 outliers final: 13 residues processed: 280 average time/residue: 0.1532 time to fit residues: 69.1647 Evaluate side-chains 274 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 258 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 634 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 187 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 262 optimal weight: 0.0570 chunk 253 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 257 optimal weight: 0.5980 chunk 87 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 GLN A 163 GLN A 625 ASN D 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.193953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148614 restraints weight = 21772.231| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.86 r_work: 0.3302 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 23172 Z= 0.101 Angle : 0.438 5.810 31328 Z= 0.236 Chirality : 0.035 0.131 3496 Planarity : 0.004 0.038 3860 Dihedral : 10.051 144.230 3296 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.83 % Allowed : 9.62 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.17), residues: 2668 helix: 1.97 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.78 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 730 TYR 0.013 0.001 TYR B 524 PHE 0.011 0.001 PHE D 540 TRP 0.013 0.001 TRP D 639 HIS 0.007 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (23152) covalent geometry : angle 0.43640 / 0.24 (31308) SS BOND : bond 0.00145 / 0.07 ( 4) SS BOND : angle 0.05080 / 0.03 ( 8) hydrogen bonds : bond 0.03739 / 2.51 ( 1384) hydrogen bonds : angle 3.36727 / 2.39 ( 4068) metal coordination : bond 0.01690 / 1.97 ( 16) metal coordination : angle 2.23319 / 1.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 0.882 Fit side-chains REVERT: C 631 ILE cc_start: 0.8133 (tp) cc_final: 0.7803 (tp) REVERT: A 631 ILE cc_start: 0.8106 (tp) cc_final: 0.7791 (tp) REVERT: B 657 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7841 (mm) REVERT: D 172 HIS cc_start: 0.6942 (OUTLIER) cc_final: 0.6114 (t-90) REVERT: D 631 ILE cc_start: 0.8166 (tp) cc_final: 0.7856 (tp) REVERT: D 715 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7247 (mp0) outliers start: 20 outliers final: 7 residues processed: 276 average time/residue: 0.1433 time to fit residues: 65.5096 Evaluate side-chains 264 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 255 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 634 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 106 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 211 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 GLN A 163 GLN B 163 GLN D 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.189931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144186 restraints weight = 21832.423| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.84 r_work: 0.3247 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23172 Z= 0.216 Angle : 0.539 5.997 31328 Z= 0.284 Chirality : 0.039 0.133 3496 Planarity : 0.004 0.044 3860 Dihedral : 10.249 144.524 3296 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.75 % Allowed : 10.16 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.17), residues: 2668 helix: 1.70 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.77 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.015 0.001 TYR B 524 PHE 0.025 0.002 PHE A 427 TRP 0.021 0.002 TRP D 315 HIS 0.007 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (23152) covalent geometry : angle 0.53632 / 0.28 (31308) SS BOND : bond 0.00010 / 0.01 ( 4) SS BOND : angle 0.18634 / 0.11 ( 8) hydrogen bonds : bond 0.04803 / 3.22 ( 1384) hydrogen bonds : angle 3.55459 / 2.52 ( 4068) metal coordination : bond 0.01737 / 1.97 ( 16) metal coordination : angle 2.62753 / 1.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 268 time to evaluate : 0.954 Fit side-chains REVERT: C 516 ASP cc_start: 0.7371 (m-30) cc_final: 0.7092 (m-30) REVERT: C 631 ILE cc_start: 0.8162 (tp) cc_final: 0.7807 (tp) REVERT: A 516 ASP cc_start: 0.7396 (m-30) cc_final: 0.7117 (m-30) REVERT: A 631 ILE cc_start: 0.8186 (tp) cc_final: 0.7841 (tp) REVERT: B 657 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8006 (mm) REVERT: D 172 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.6187 (t-90) REVERT: D 631 ILE cc_start: 0.8177 (tp) cc_final: 0.7839 (tp) REVERT: D 657 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7956 (mm) outliers start: 18 outliers final: 12 residues processed: 278 average time/residue: 0.1463 time to fit residues: 66.8537 Evaluate side-chains 269 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 97 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 GLN A 163 GLN A 742 ASN B 163 GLN D 163 GLN D 309 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.191928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146797 restraints weight = 21728.752| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.83 r_work: 0.3283 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23172 Z= 0.148 Angle : 0.480 5.959 31328 Z= 0.257 Chirality : 0.037 0.130 3496 Planarity : 0.004 0.043 3860 Dihedral : 10.039 143.122 3296 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.75 % Allowed : 11.11 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.17), residues: 2668 helix: 1.81 (0.12), residues: 1916 sheet: None (None), residues: 0 loop : -0.79 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.013 0.001 TYR B 524 PHE 0.014 0.001 PHE B 427 TRP 0.017 0.001 TRP B 315 HIS 0.007 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (23152) covalent geometry : angle 0.47756 / 0.26 (31308) SS BOND : bond 0.00090 / 0.05 ( 4) SS BOND : angle 0.16352 / 0.10 ( 8) hydrogen bonds : bond 0.04169 / 2.79 ( 1384) hydrogen bonds : angle 3.48536 / 2.47 ( 4068) metal coordination : bond 0.01609 / 1.86 ( 16) metal coordination : angle 2.32574 / 1.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 265 time to evaluate : 0.873 Fit side-chains REVERT: C 427 PHE cc_start: 0.7829 (t80) cc_final: 0.7574 (t80) REVERT: C 631 ILE cc_start: 0.8162 (tp) cc_final: 0.7836 (tp) REVERT: A 172 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.6101 (t-90) REVERT: A 427 PHE cc_start: 0.7951 (t80) cc_final: 0.7718 (t80) REVERT: A 631 ILE cc_start: 0.8203 (tp) cc_final: 0.7887 (tp) REVERT: B 657 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7999 (mm) REVERT: D 172 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6127 (t-90) REVERT: D 631 ILE cc_start: 0.8213 (tp) cc_final: 0.7894 (tp) REVERT: D 657 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7987 (mm) outliers start: 18 outliers final: 8 residues processed: 275 average time/residue: 0.1461 time to fit residues: 66.2132 Evaluate side-chains 263 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 251 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 90 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 103 optimal weight: 0.0670 chunk 125 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 GLN C 742 ASN A 163 GLN B 163 GLN D 163 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.193113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.148666 restraints weight = 21665.254| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.80 r_work: 0.3280 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23172 Z= 0.126 Angle : 0.460 6.359 31328 Z= 0.248 Chirality : 0.036 0.128 3496 Planarity : 0.004 0.041 3860 Dihedral : 9.842 141.169 3296 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.75 % Allowed : 11.40 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.17), residues: 2668 helix: 1.94 (0.12), residues: 1916 sheet: None (None), residues: 0 loop : -0.75 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.013 0.001 TYR B 524 PHE 0.025 0.001 PHE D 427 TRP 0.016 0.001 TRP B 315 HIS 0.006 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (23152) covalent geometry : angle 0.45789 / 0.25 (31308) SS BOND : bond 0.00097 / 0.05 ( 4) SS BOND : angle 0.14050 / 0.08 ( 8) hydrogen bonds : bond 0.03896 / 2.61 ( 1384) hydrogen bonds : angle 3.43708 / 2.44 ( 4068) metal coordination : bond 0.01503 / 1.75 ( 16) metal coordination : angle 2.12778 / 1.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 262 time to evaluate : 0.841 Fit side-chains REVERT: C 631 ILE cc_start: 0.8168 (tp) cc_final: 0.7842 (tp) REVERT: A 172 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.6063 (t-90) REVERT: A 631 ILE cc_start: 0.8195 (tp) cc_final: 0.7882 (tp) REVERT: A 715 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7275 (mp0) REVERT: B 657 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7967 (mm) REVERT: D 172 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.6060 (t-90) REVERT: D 551 ASN cc_start: 0.8139 (t0) cc_final: 0.7899 (t0) REVERT: D 631 ILE cc_start: 0.8233 (tp) cc_final: 0.7921 (tp) REVERT: D 657 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7944 (mm) outliers start: 18 outliers final: 9 residues processed: 272 average time/residue: 0.1449 time to fit residues: 65.1040 Evaluate side-chains 261 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 248 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 217 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 236 optimal weight: 0.0870 chunk 256 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 GLN A 163 GLN B 163 GLN D 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.193385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.148001 restraints weight = 21719.048| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.87 r_work: 0.3298 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23172 Z= 0.125 Angle : 0.461 5.915 31328 Z= 0.249 Chirality : 0.036 0.147 3496 Planarity : 0.004 0.040 3860 Dihedral : 9.789 141.277 3296 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.66 % Allowed : 11.61 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.17), residues: 2668 helix: 2.00 (0.12), residues: 1916 sheet: None (None), residues: 0 loop : -0.73 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 730 TYR 0.013 0.001 TYR B 524 PHE 0.026 0.001 PHE B 427 TRP 0.016 0.001 TRP B 315 HIS 0.006 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (23152) covalent geometry : angle 0.45947 / 0.25 (31308) SS BOND : bond 0.00086 / 0.04 ( 4) SS BOND : angle 0.14443 / 0.09 ( 8) hydrogen bonds : bond 0.03860 / 2.59 ( 1384) hydrogen bonds : angle 3.43200 / 2.43 ( 4068) metal coordination : bond 0.01472 / 1.71 ( 16) metal coordination : angle 2.10842 / 1.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 261 time to evaluate : 0.871 Fit side-chains REVERT: C 631 ILE cc_start: 0.8165 (tp) cc_final: 0.7842 (tp) REVERT: A 172 HIS cc_start: 0.6973 (OUTLIER) cc_final: 0.6070 (t-90) REVERT: A 551 ASN cc_start: 0.8086 (t0) cc_final: 0.7847 (t0) REVERT: A 631 ILE cc_start: 0.8214 (tp) cc_final: 0.7900 (tp) REVERT: A 715 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7252 (mp0) REVERT: B 551 ASN cc_start: 0.8076 (t0) cc_final: 0.7836 (t0) REVERT: B 657 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7984 (mm) REVERT: B 715 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7379 (mp0) REVERT: D 172 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6034 (t-90) REVERT: D 551 ASN cc_start: 0.8088 (t0) cc_final: 0.7846 (t0) REVERT: D 631 ILE cc_start: 0.8235 (tp) cc_final: 0.7919 (tp) REVERT: D 657 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7966 (mm) outliers start: 16 outliers final: 11 residues processed: 269 average time/residue: 0.1476 time to fit residues: 65.3666 Evaluate side-chains 266 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 167 optimal weight: 0.5980 chunk 161 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 GLN A 163 GLN B 163 GLN D 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.193408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.148378 restraints weight = 21768.678| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.85 r_work: 0.3288 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23172 Z= 0.128 Angle : 0.463 5.906 31328 Z= 0.249 Chirality : 0.036 0.146 3496 Planarity : 0.004 0.040 3860 Dihedral : 9.779 141.305 3296 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.62 % Allowed : 11.48 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.17), residues: 2668 helix: 2.04 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.76 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.013 0.001 TYR B 524 PHE 0.031 0.001 PHE C 427 TRP 0.016 0.001 TRP D 315 HIS 0.006 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (23152) covalent geometry : angle 0.46091 / 0.25 (31308) SS BOND : bond 0.00082 / 0.04 ( 4) SS BOND : angle 0.15302 / 0.09 ( 8) hydrogen bonds : bond 0.03880 / 2.60 ( 1384) hydrogen bonds : angle 3.42358 / 2.43 ( 4068) metal coordination : bond 0.01471 / 1.72 ( 16) metal coordination : angle 2.12761 / 1.16 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 259 time to evaluate : 0.913 Fit side-chains REVERT: C 631 ILE cc_start: 0.8170 (tp) cc_final: 0.7843 (tp) REVERT: A 115 LEU cc_start: 0.8481 (mp) cc_final: 0.8226 (mp) REVERT: A 172 HIS cc_start: 0.6947 (OUTLIER) cc_final: 0.6067 (t-90) REVERT: A 551 ASN cc_start: 0.8139 (t0) cc_final: 0.7898 (t0) REVERT: A 631 ILE cc_start: 0.8228 (tp) cc_final: 0.7913 (tp) REVERT: A 715 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7265 (mp0) REVERT: B 551 ASN cc_start: 0.8098 (t0) cc_final: 0.7855 (t0) REVERT: B 657 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7999 (mm) REVERT: B 715 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7404 (mp0) REVERT: D 172 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.6025 (t-90) REVERT: D 551 ASN cc_start: 0.8100 (t0) cc_final: 0.7858 (t0) REVERT: D 631 ILE cc_start: 0.8247 (tp) cc_final: 0.7931 (tp) REVERT: D 657 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7985 (mm) outliers start: 15 outliers final: 10 residues processed: 265 average time/residue: 0.1461 time to fit residues: 63.9647 Evaluate side-chains 264 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 250 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 237 optimal weight: 0.5980 chunk 234 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 216 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 163 GLN A 163 GLN B 163 GLN D 163 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.192776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147998 restraints weight = 21671.527| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.82 r_work: 0.3267 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23172 Z= 0.148 Angle : 0.481 5.955 31328 Z= 0.258 Chirality : 0.037 0.136 3496 Planarity : 0.004 0.041 3860 Dihedral : 9.873 141.713 3296 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.62 % Allowed : 11.57 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.17), residues: 2668 helix: 1.97 (0.12), residues: 1916 sheet: None (None), residues: 0 loop : -0.77 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 170 TYR 0.014 0.001 TYR B 524 PHE 0.024 0.001 PHE B 427 TRP 0.017 0.001 TRP A 315 HIS 0.006 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (23152) covalent geometry : angle 0.47919 / 0.26 (31308) SS BOND : bond 0.00064 / 0.03 ( 4) SS BOND : angle 0.19129 / 0.11 ( 8) hydrogen bonds : bond 0.04059 / 2.72 ( 1384) hydrogen bonds : angle 3.44306 / 2.44 ( 4068) metal coordination : bond 0.01500 / 1.74 ( 16) metal coordination : angle 2.20632 / 1.20 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4577.04 seconds wall clock time: 79 minutes 41.41 seconds (4781.41 seconds total)