Starting phenix.real_space_refine on Sun Aug 24 22:33:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x6c_33021/08_2025/7x6c_33021.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x6c_33021/08_2025/7x6c_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_33021/08_2025/7x6c_33021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x6c_33021/08_2025/7x6c_33021.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x6c_33021/08_2025/7x6c_33021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x6c_33021/08_2025/7x6c_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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22632 Number of models: 1 Model: "" Number of chains: 5 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: "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 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 Restraints were copied for chains: B, C, D Time building chain proxies: 5.63, per 1000 atoms: 0.25 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.4 microseconds 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: 0.57 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: 3.06 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: 13735 35.59 - 71.19: 341 71.19 - 106.78: 23 106.78 - 142.38: 20 142.38 - 177.97: 4 Dihedral angle restraints: 14123 sinusoidal: 6127 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 14120 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: 2.03 - 2.60: 127 2.60 - 3.18: 18159 3.18 - 3.75: 34722 3.75 - 4.33: 46734 4.33 - 4.90: 80688 Nonbonded interactions: 180430 Sorted by model distance: nonbonded pdb=" SG CYS B 553 " pdb=" SG CYS B 558 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 553 " pdb=" SG CYS D 558 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS A 553 " pdb=" SG CYS A 558 " model vdw 2.031 3.760 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 ... (remaining 180425 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: 0.02 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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.910 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 23169 Z= 0.210 Angle : 0.736 11.426 31322 Z= 0.383 Chirality : 0.042 0.219 3496 Planarity : 0.006 0.067 3860 Dihedral : 16.820 177.972 8920 Min Nonbonded Distance : 2.031 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 aren 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 covalent geometry : bond 0.00443 (23152) covalent geometry : angle 0.73522 (31308) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.21090 ( 2) hydrogen bonds : bond 0.13342 ( 1384) hydrogen bonds : angle 4.86465 ( 4068) metal coordination : bond 0.01145 ( 16) metal coordination : angle 1.83889 ( 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 : 0.746 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: 0.1227 time to fit residues: 63.3904 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 : 0.621 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 629 GLN A 163 GLN A 625 ASN A 629 GLN B 163 GLN B 432 HIS B 625 ASN D 163 GLN D 625 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.196866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.151961 restraints weight = 22217.150| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.83 r_work: 0.3371 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 23169 Z= 0.116 Angle : 0.465 5.359 31322 Z= 0.248 Chirality : 0.036 0.132 3496 Planarity : 0.004 0.050 3860 Dihedral : 12.627 147.576 3606 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.66 % Allowed : 3.90 % Favored : 95.44 % 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 aren not related in a simple way. whole: 1.16 (0.16), residues: 2668 helix: 1.46 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -0.94 (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 0.013 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 covalent geometry : bond 0.00262 (23152) covalent geometry : angle 0.46372 (31308) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.36016 ( 2) hydrogen bonds : bond 0.04009 ( 1384) hydrogen bonds : angle 3.45327 ( 4068) metal coordination : bond 0.03269 ( 16) metal coordination : angle 2.01894 ( 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 296 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 280 time to evaluate : 0.745 Fit side-chains REVERT: C 349 LEU cc_start: 0.8484 (mt) cc_final: 0.8196 (mt) REVERT: A 349 LEU cc_start: 0.8438 (mt) cc_final: 0.8108 (mt) REVERT: A 631 ILE cc_start: 0.8126 (tp) cc_final: 0.7725 (tp) REVERT: D 66 MET cc_start: 0.6153 (ttt) cc_final: 0.5838 (tpp) REVERT: D 172 HIS cc_start: 0.7190 (OUTLIER) cc_final: 0.6312 (t-90) REVERT: D 349 LEU cc_start: 0.8476 (mt) cc_final: 0.8154 (mt) REVERT: D 355 ASN cc_start: 0.7746 (t0) cc_final: 0.7546 (t0) REVERT: D 516 ASP cc_start: 0.7139 (m-30) cc_final: 0.6677 (m-30) REVERT: D 631 ILE cc_start: 0.8125 (tp) cc_final: 0.7800 (tp) outliers start: 16 outliers final: 5 residues processed: 290 average time/residue: 0.1184 time to fit residues: 56.6214 Evaluate side-chains 267 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 261 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 634 HIS Chi-restraints excluded: chain D residue 172 HIS 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: 0.7980 chunk 50 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 171 optimal weight: 0.0270 chunk 81 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 625 ASN C 629 GLN C 742 ASN B 742 ASN D 163 GLN D 432 HIS D 625 ASN D 742 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.196158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.151922 restraints weight = 22136.992| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.73 r_work: 0.3349 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23169 Z= 0.108 Angle : 0.439 5.735 31322 Z= 0.232 Chirality : 0.036 0.153 3496 Planarity : 0.004 0.044 3860 Dihedral : 11.123 146.781 3600 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.70 % Allowed : 5.06 % Favored : 94.24 % 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 aren not related in a simple way. whole: 1.71 (0.16), residues: 2668 helix: 1.91 (0.12), residues: 1904 sheet: None (None), residues: 0 loop : -0.87 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 730 TYR 0.014 0.001 TYR A 524 PHE 0.022 0.001 PHE A 427 TRP 0.013 0.001 TRP C 315 HIS 0.007 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00249 (23152) covalent geometry : angle 0.43630 (31308) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.11969 ( 2) hydrogen bonds : bond 0.03720 ( 1384) hydrogen bonds : angle 3.34197 ( 4068) metal coordination : bond 0.02037 ( 16) metal coordination : angle 2.36095 ( 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 294 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 277 time to evaluate : 0.651 Fit side-chains REVERT: C 349 LEU cc_start: 0.8272 (mt) cc_final: 0.8006 (mt) REVERT: C 355 ASN cc_start: 0.7745 (t0) cc_final: 0.7541 (t0) REVERT: C 516 ASP cc_start: 0.7286 (m-30) cc_final: 0.6998 (m-30) REVERT: C 631 ILE cc_start: 0.8157 (tp) cc_final: 0.7764 (tp) REVERT: A 197 LEU cc_start: 0.8885 (tp) cc_final: 0.8673 (tp) REVERT: A 349 LEU cc_start: 0.8189 (mt) cc_final: 0.7921 (mt) REVERT: A 516 ASP cc_start: 0.7272 (m-30) cc_final: 0.7034 (m-30) REVERT: A 558 CYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8205 (m) REVERT: A 631 ILE cc_start: 0.8137 (tp) cc_final: 0.7796 (tp) REVERT: B 197 LEU cc_start: 0.8853 (tp) cc_final: 0.8603 (tp) REVERT: B 349 LEU cc_start: 0.8401 (mt) cc_final: 0.8168 (mt) REVERT: D 66 MET cc_start: 0.6106 (ttt) cc_final: 0.5873 (ttt) REVERT: D 172 HIS cc_start: 0.6991 (OUTLIER) cc_final: 0.6192 (t-90) REVERT: D 197 LEU cc_start: 0.8835 (tp) cc_final: 0.8588 (tp) REVERT: D 349 LEU cc_start: 0.8426 (mt) cc_final: 0.8118 (mt) REVERT: D 631 ILE cc_start: 0.8136 (tp) cc_final: 0.7840 (tp) outliers start: 17 outliers final: 9 residues processed: 288 average time/residue: 0.1160 time to fit residues: 54.9111 Evaluate side-chains 277 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 266 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 558 CYS 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: 0.7980 chunk 11 optimal weight: 0.4980 chunk 149 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 ASN B 742 ASN D 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.191545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146207 restraints weight = 21950.906| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.90 r_work: 0.3273 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23169 Z= 0.195 Angle : 0.518 5.734 31322 Z= 0.272 Chirality : 0.038 0.133 3496 Planarity : 0.004 0.042 3860 Dihedral : 11.061 147.946 3600 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.04 % Allowed : 6.84 % Favored : 92.12 % 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 aren not related in a simple way. whole: 1.59 (0.16), residues: 2668 helix: 1.77 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.79 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 730 TYR 0.015 0.001 TYR B 524 PHE 0.023 0.002 PHE B 427 TRP 0.020 0.002 TRP C 315 HIS 0.007 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00479 (23152) covalent geometry : angle 0.51539 (31308) SS BOND : bond 0.00007 ( 1) SS BOND : angle 0.22324 ( 2) hydrogen bonds : bond 0.04618 ( 1384) hydrogen bonds : angle 3.40970 ( 4068) metal coordination : bond 0.01937 ( 16) metal coordination : angle 2.60959 ( 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 292 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 0.602 Fit side-chains REVERT: C 349 LEU cc_start: 0.8352 (mt) cc_final: 0.8077 (mt) REVERT: C 631 ILE cc_start: 0.8219 (tp) cc_final: 0.7833 (tp) REVERT: C 730 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7370 (ttt-90) REVERT: A 355 ASN cc_start: 0.7714 (t0) cc_final: 0.7495 (t0) REVERT: A 516 ASP cc_start: 0.7341 (m-30) cc_final: 0.7091 (m-30) REVERT: A 631 ILE cc_start: 0.8235 (tp) cc_final: 0.7847 (tp) REVERT: A 730 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7343 (ttt-90) REVERT: B 657 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7747 (mm) REVERT: B 730 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7355 (ttt-90) REVERT: D 66 MET cc_start: 0.6240 (ttt) cc_final: 0.5949 (ttt) REVERT: D 172 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6239 (t-90) REVERT: D 516 ASP cc_start: 0.7318 (m-30) cc_final: 0.7050 (m-30) REVERT: D 625 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7701 (t0) REVERT: D 631 ILE cc_start: 0.8197 (tp) cc_final: 0.7884 (tp) outliers start: 25 outliers final: 13 residues processed: 277 average time/residue: 0.1174 time to fit residues: 52.3071 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 : 0.554 ------------------------------------------------------------------------------- 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 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 625 ASN 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: 0.9980 chunk 116 optimal weight: 0.6980 chunk 262 optimal weight: 0.8980 chunk 253 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 625 ASN A 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.193283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147824 restraints weight = 21802.620| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.81 r_work: 0.3310 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23169 Z= 0.128 Angle : 0.458 5.792 31322 Z= 0.244 Chirality : 0.036 0.130 3496 Planarity : 0.004 0.040 3860 Dihedral : 10.794 147.890 3600 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.75 % Allowed : 8.75 % Favored : 90.51 % 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 aren not related in a simple way. whole: 1.79 (0.17), residues: 2668 helix: 1.94 (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 0.003 0.000 ARG C 730 TYR 0.013 0.001 TYR D 524 PHE 0.024 0.001 PHE A 427 TRP 0.015 0.001 TRP C 315 HIS 0.007 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00302 (23152) covalent geometry : angle 0.45544 (31308) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.12606 ( 2) hydrogen bonds : bond 0.03969 ( 1384) hydrogen bonds : angle 3.35091 ( 4068) metal coordination : bond 0.01753 ( 16) metal coordination : angle 2.40003 ( 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 280 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 262 time to evaluate : 0.670 Fit side-chains REVERT: C 349 LEU cc_start: 0.8324 (mt) cc_final: 0.8075 (mt) REVERT: C 516 ASP cc_start: 0.7254 (m-30) cc_final: 0.6949 (m-30) REVERT: C 631 ILE cc_start: 0.8103 (tp) cc_final: 0.7741 (tp) REVERT: A 516 ASP cc_start: 0.7345 (m-30) cc_final: 0.7059 (m-30) REVERT: A 631 ILE cc_start: 0.8128 (tp) cc_final: 0.7784 (tp) REVERT: B 657 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7765 (mm) REVERT: B 730 ARG cc_start: 0.7728 (ttp80) cc_final: 0.7334 (ttt-90) REVERT: D 66 MET cc_start: 0.6209 (ttt) cc_final: 0.5944 (ttt) REVERT: D 172 HIS cc_start: 0.6959 (OUTLIER) cc_final: 0.6131 (t-90) REVERT: D 631 ILE cc_start: 0.8179 (tp) cc_final: 0.7860 (tp) outliers start: 18 outliers final: 12 residues processed: 269 average time/residue: 0.1222 time to fit residues: 53.5557 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 : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 MET 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=3.00 ------------------------------------------------------------------------------- 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: 0.7980 chunk 211 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN A 742 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.191212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146678 restraints weight = 21827.955| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.90 r_work: 0.3252 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23169 Z= 0.183 Angle : 0.511 5.872 31322 Z= 0.269 Chirality : 0.038 0.131 3496 Planarity : 0.004 0.042 3860 Dihedral : 10.896 150.295 3600 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.95 % Allowed : 9.83 % Favored : 89.22 % 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 aren not related in a simple way. whole: 1.66 (0.17), residues: 2668 helix: 1.83 (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 0.003 0.000 ARG A 730 TYR 0.014 0.001 TYR B 524 PHE 0.013 0.002 PHE B 427 TRP 0.020 0.002 TRP D 315 HIS 0.007 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00450 (23152) covalent geometry : angle 0.50900 (31308) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.22942 ( 2) hydrogen bonds : bond 0.04537 ( 1384) hydrogen bonds : angle 3.40142 ( 4068) metal coordination : bond 0.01762 ( 16) metal coordination : angle 2.51581 ( 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 283 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 0.799 Fit side-chains REVERT: C 427 PHE cc_start: 0.7926 (t80) cc_final: 0.7694 (t80) REVERT: C 619 MET cc_start: 0.7994 (ttt) cc_final: 0.7779 (ttt) REVERT: C 631 ILE cc_start: 0.8183 (tp) cc_final: 0.7824 (tp) REVERT: A 66 MET cc_start: 0.6281 (ttt) cc_final: 0.6037 (ttt) REVERT: A 172 HIS cc_start: 0.7090 (OUTLIER) cc_final: 0.6157 (t-90) REVERT: A 516 ASP cc_start: 0.7421 (m-30) cc_final: 0.7139 (m-30) REVERT: A 631 ILE cc_start: 0.8204 (tp) cc_final: 0.7847 (tp) REVERT: A 715 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7365 (mp0) REVERT: B 657 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7935 (mm) REVERT: D 172 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.6189 (t-90) REVERT: D 631 ILE cc_start: 0.8198 (tp) cc_final: 0.7858 (tp) REVERT: D 657 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7907 (mm) outliers start: 23 outliers final: 12 residues processed: 270 average time/residue: 0.1149 time to fit residues: 51.1445 Evaluate side-chains 266 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 250 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 192 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 180 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN A 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.192723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147511 restraints weight = 21722.473| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.81 r_work: 0.3284 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23169 Z= 0.136 Angle : 0.466 5.891 31322 Z= 0.250 Chirality : 0.036 0.128 3496 Planarity : 0.004 0.041 3860 Dihedral : 10.665 150.688 3600 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.95 % Allowed : 10.03 % Favored : 89.01 % 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 aren not related in a simple way. whole: 1.78 (0.17), residues: 2668 helix: 1.93 (0.12), residues: 1916 sheet: None (None), residues: 0 loop : -0.78 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 730 TYR 0.013 0.001 TYR A 524 PHE 0.022 0.001 PHE A 427 TRP 0.016 0.001 TRP B 315 HIS 0.006 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00325 (23152) covalent geometry : angle 0.46417 (31308) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.11721 ( 2) hydrogen bonds : bond 0.04024 ( 1384) hydrogen bonds : angle 3.38384 ( 4068) metal coordination : bond 0.01599 ( 16) metal coordination : angle 2.26973 ( 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 289 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 266 time to evaluate : 0.712 Fit side-chains REVERT: C 427 PHE cc_start: 0.7995 (t80) cc_final: 0.7755 (t80) REVERT: C 631 ILE cc_start: 0.8140 (tp) cc_final: 0.7809 (tp) REVERT: C 741 GLU cc_start: 0.7982 (tp30) cc_final: 0.7772 (tt0) REVERT: A 66 MET cc_start: 0.6093 (ttt) cc_final: 0.5840 (ttt) REVERT: A 172 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6109 (t-90) REVERT: A 631 ILE cc_start: 0.8172 (tp) cc_final: 0.7836 (tp) REVERT: A 715 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7281 (mp0) REVERT: B 657 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7911 (mm) REVERT: D 172 HIS cc_start: 0.6915 (OUTLIER) cc_final: 0.6097 (t-90) REVERT: D 309 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: D 631 ILE cc_start: 0.8186 (tp) cc_final: 0.7860 (tp) REVERT: D 657 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7892 (mm) outliers start: 23 outliers final: 13 residues processed: 279 average time/residue: 0.1125 time to fit residues: 52.0035 Evaluate side-chains 276 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 258 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 343 MET 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 309 GLN Chi-restraints excluded: chain D residue 343 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 90 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 31 optimal weight: 0.0070 chunk 103 optimal weight: 0.0970 chunk 125 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 214 optimal weight: 0.4980 chunk 192 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN A 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.195573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150555 restraints weight = 21651.281| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.79 r_work: 0.3344 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 23169 Z= 0.097 Angle : 0.430 6.384 31322 Z= 0.235 Chirality : 0.035 0.135 3496 Planarity : 0.003 0.037 3860 Dihedral : 10.237 149.959 3600 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.62 % Allowed : 10.95 % Favored : 88.43 % 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 aren not related in a simple way. whole: 2.03 (0.17), residues: 2668 helix: 2.14 (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 0.003 0.000 ARG B 730 TYR 0.013 0.001 TYR B 524 PHE 0.026 0.001 PHE D 427 TRP 0.013 0.001 TRP D 315 HIS 0.006 0.000 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00214 (23152) covalent geometry : angle 0.42863 (31308) SS BOND : bond 0.00095 ( 1) SS BOND : angle 0.03427 ( 2) hydrogen bonds : bond 0.03436 ( 1384) hydrogen bonds : angle 3.38099 ( 4068) metal coordination : bond 0.01400 ( 16) metal coordination : angle 1.91449 ( 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 289 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 274 time to evaluate : 0.841 Fit side-chains REVERT: C 393 LEU cc_start: 0.8385 (mt) cc_final: 0.8138 (mp) REVERT: C 631 ILE cc_start: 0.8148 (tp) cc_final: 0.7827 (tp) REVERT: C 715 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7227 (mp0) REVERT: C 741 GLU cc_start: 0.7974 (tp30) cc_final: 0.7690 (tt0) REVERT: A 172 HIS cc_start: 0.6944 (OUTLIER) cc_final: 0.6007 (t-90) REVERT: A 393 LEU cc_start: 0.8338 (mt) cc_final: 0.8089 (mp) REVERT: A 631 ILE cc_start: 0.8169 (tp) cc_final: 0.7853 (tp) REVERT: A 715 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7246 (mp0) REVERT: B 393 LEU cc_start: 0.8425 (mt) cc_final: 0.8157 (mp) REVERT: B 631 ILE cc_start: 0.8229 (tp) cc_final: 0.7935 (tp) REVERT: B 657 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7835 (mm) REVERT: B 715 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7322 (mp0) REVERT: D 172 HIS cc_start: 0.6852 (OUTLIER) cc_final: 0.6035 (t-90) REVERT: D 631 ILE cc_start: 0.8211 (tp) cc_final: 0.7913 (tp) REVERT: D 657 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7811 (mm) REVERT: D 715 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7291 (mp0) outliers start: 15 outliers final: 6 residues processed: 283 average time/residue: 0.1102 time to fit residues: 51.6370 Evaluate side-chains 269 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 259 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 172 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 343 MET 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: 1.9990 chunk 193 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 625 ASN A 163 GLN A 625 ASN B 309 GLN B 625 ASN D 309 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.190929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145465 restraints weight = 21793.508| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.86 r_work: 0.3264 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23169 Z= 0.208 Angle : 0.537 5.998 31322 Z= 0.284 Chirality : 0.039 0.130 3496 Planarity : 0.004 0.043 3860 Dihedral : 10.697 151.230 3600 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.79 % Allowed : 10.66 % Favored : 88.56 % 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 aren not related in a simple way. whole: 1.62 (0.16), residues: 2668 helix: 1.80 (0.12), residues: 1920 sheet: None (None), residues: 0 loop : -0.82 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 730 TYR 0.015 0.001 TYR B 524 PHE 0.030 0.002 PHE C 427 TRP 0.021 0.002 TRP B 315 HIS 0.006 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00515 (23152) covalent geometry : angle 0.53451 (31308) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.22000 ( 2) hydrogen bonds : bond 0.04660 ( 1384) hydrogen bonds : angle 3.52203 ( 4068) metal coordination : bond 0.01650 ( 16) metal coordination : angle 2.48158 ( 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 278 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 259 time to evaluate : 0.781 Fit side-chains REVERT: C 631 ILE cc_start: 0.8204 (tp) cc_final: 0.7857 (tp) REVERT: C 715 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7249 (mp0) REVERT: C 741 GLU cc_start: 0.8000 (tp30) cc_final: 0.7734 (tt0) REVERT: A 172 HIS cc_start: 0.7054 (OUTLIER) cc_final: 0.6147 (t-90) REVERT: A 631 ILE cc_start: 0.8225 (tp) cc_final: 0.7880 (tp) REVERT: A 715 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7275 (mp0) REVERT: B 309 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: B 657 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8050 (mm) REVERT: D 172 HIS cc_start: 0.6991 (OUTLIER) cc_final: 0.6179 (t-90) REVERT: D 309 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: D 631 ILE cc_start: 0.8226 (tp) cc_final: 0.7878 (tp) REVERT: D 657 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8007 (mm) outliers start: 19 outliers final: 9 residues processed: 270 average time/residue: 0.1151 time to fit residues: 50.8942 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 : 0.698 ------------------------------------------------------------------------------- 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 634 HIS Chi-restraints excluded: chain B residue 309 GLN 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 309 GLN Chi-restraints excluded: chain D residue 343 MET 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: 0.9980 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 252 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN A 163 GLN A 742 ASN B 163 GLN B 309 GLN D 163 GLN D 309 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.193388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147670 restraints weight = 21778.906| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.85 r_work: 0.3297 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23169 Z= 0.123 Angle : 0.467 5.930 31322 Z= 0.252 Chirality : 0.036 0.128 3496 Planarity : 0.004 0.041 3860 Dihedral : 10.488 151.429 3600 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.58 % Allowed : 11.03 % Favored : 88.39 % 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 aren 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 0.003 0.000 ARG C 730 TYR 0.013 0.001 TYR B 524 PHE 0.011 0.001 PHE B 540 TRP 0.015 0.001 TRP D 315 HIS 0.007 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00290 (23152) covalent geometry : angle 0.46500 (31308) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.10143 ( 2) hydrogen bonds : bond 0.03906 ( 1384) hydrogen bonds : angle 3.45089 ( 4068) metal coordination : bond 0.01496 ( 16) metal coordination : angle 2.12453 ( 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 275 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 261 time to evaluate : 0.699 Fit side-chains REVERT: C 427 PHE cc_start: 0.7775 (t80) cc_final: 0.7569 (t80) REVERT: C 551 ASN cc_start: 0.8112 (t0) cc_final: 0.7878 (t0) REVERT: C 631 ILE cc_start: 0.8183 (tp) cc_final: 0.7866 (tp) REVERT: C 715 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7245 (mp0) REVERT: C 741 GLU cc_start: 0.7986 (tp30) cc_final: 0.7704 (tt0) REVERT: A 172 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6050 (t-90) REVERT: A 631 ILE cc_start: 0.8178 (tp) cc_final: 0.7854 (tp) REVERT: A 715 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7213 (mp0) REVERT: B 631 ILE cc_start: 0.8270 (tp) cc_final: 0.7989 (tp) REVERT: B 657 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7989 (mm) REVERT: D 172 HIS cc_start: 0.6888 (OUTLIER) cc_final: 0.6089 (t-90) REVERT: D 631 ILE cc_start: 0.8242 (tp) cc_final: 0.7944 (tp) REVERT: D 657 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7937 (mm) REVERT: D 715 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7326 (mp0) outliers start: 14 outliers final: 7 residues processed: 269 average time/residue: 0.1123 time to fit residues: 49.3891 Evaluate side-chains 263 residues out of total 2412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 252 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.6980 chunk 234 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 232 optimal weight: 0.1980 chunk 224 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 216 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4134 r_free = 0.4134 target = 0.194300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148960 restraints weight = 21701.480| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.85 r_work: 0.3306 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23169 Z= 0.117 Angle : 0.455 5.880 31322 Z= 0.246 Chirality : 0.036 0.135 3496 Planarity : 0.004 0.039 3860 Dihedral : 10.267 151.013 3600 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.50 % Allowed : 11.32 % Favored : 88.18 % 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 aren not related in a simple way. whole: 1.96 (0.17), residues: 2668 helix: 2.09 (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 A 730 TYR 0.013 0.001 TYR D 524 PHE 0.011 0.001 PHE A 540 TRP 0.015 0.001 TRP D 315 HIS 0.006 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00274 (23152) covalent geometry : angle 0.45305 (31308) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.08047 ( 2) hydrogen bonds : bond 0.03727 ( 1384) hydrogen bonds : angle 3.41326 ( 4068) metal coordination : bond 0.01446 ( 16) metal coordination : angle 2.04247 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3659.09 seconds wall clock time: 63 minutes 47.93 seconds (3827.93 seconds total)