Starting phenix.real_space_refine on Sat Jul 4 19:27:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wdb_32436/07_2026/7wdb_32436.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wdb_32436/07_2026/7wdb_32436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wdb_32436/07_2026/7wdb_32436.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wdb_32436/07_2026/7wdb_32436.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wdb_32436/07_2026/7wdb_32436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wdb_32436/07_2026/7wdb_32436.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wdb_32436/07_2026/7wdb_32436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wdb_32436/07_2026/7wdb_32436.map" } resolution = 2.4 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 120 5.16 5 C 14708 2.51 5 N 3580 2.21 5 O 3964 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 22400 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5420 Classifications: {'peptide': 665} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 640} Chain breaks: 5 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {' CA': 1, ' ZN': 1, '657': 1, '7OC': 1, 'POV': 1, 'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS A 176 41.628 98.102 61.300 1.00112.72 S ATOM 1162 SG CYS A 178 38.798 99.317 59.044 1.00134.61 S ATOM 1184 SG CYS A 181 39.622 95.636 59.173 1.00136.41 S Restraints were copied for chains: B, C, D Time building chain proxies: 6.29, per 1000 atoms: 0.28 Number of scatterers: 22400 At special positions: 0 Unit cell: (114.119, 114.119, 136.286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 120 16.00 P 8 15.00 F 12 9.00 O 3964 8.00 N 3580 7.00 C 14708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.04 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.04 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.04 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 804.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 176 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 176 " pdb=" ZN C 903 " pdb="ZN ZN C 903 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 178 " pdb=" ZN D 903 " pdb="ZN ZN D 903 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 903 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 903 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 903 " - pdb=" SG CYS D 176 " Number of angles added : 12 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5128 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 4 sheets defined 78.5% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.501A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 401 through 426 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 434 through 460 removed outlier: 3.831A pdb=" N MET A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.659A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 3.781A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.151A 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 545 through 549 Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.659A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.500A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'A' and resid 615 through 633 removed outlier: 4.406A pdb=" N ASP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 650 removed outlier: 3.661A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 734 Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.501A pdb=" N GLU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 362 through 384 Processing helix chain 'B' and resid 401 through 426 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 434 through 460 removed outlier: 3.831A pdb=" N MET B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.659A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 3.781A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.151A 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 545 through 549 Processing helix chain 'B' and resid 567 through 580 removed outlier: 3.660A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.500A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'B' and resid 615 through 633 removed outlier: 4.408A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 650 removed outlier: 3.661A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 734 Processing helix chain 'B' and resid 740 through 761 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.501A pdb=" N GLU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 401 through 426 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 434 through 460 removed outlier: 3.830A pdb=" N MET C 438 " --> pdb=" O TRP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.659A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 3.781A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.151A 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 545 through 549 Processing helix chain 'C' and resid 567 through 580 removed outlier: 3.659A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.500A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'C' and resid 615 through 633 removed outlier: 4.406A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 650 removed outlier: 3.661A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 734 Processing helix chain 'C' and resid 740 through 761 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.501A pdb=" N GLU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 108 through 117 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 362 through 384 Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 434 through 460 removed outlier: 3.831A pdb=" N MET D 438 " --> pdb=" O TRP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.659A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 3.781A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.151A 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 545 through 549 Processing helix chain 'D' and resid 567 through 580 removed outlier: 3.659A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE D 580 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.500A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 615 Processing helix chain 'D' and resid 615 through 633 removed outlier: 4.407A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 650 removed outlier: 3.661A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 734 Processing helix chain 'D' and resid 740 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.434A pdb=" N VAL C 166 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.434A pdb=" N VAL A 166 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.434A pdb=" N VAL D 166 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 166 through 168 removed outlier: 4.434A pdb=" N VAL B 166 " --> pdb=" O LEU C 20 " (cutoff:3.500A) 1480 hydrogen bonds defined for protein. 4308 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: 3.92 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: 1.19 - 1.44: 9700 1.44 - 1.70: 13012 1.70 - 1.95: 188 1.95 - 2.20: 0 2.20 - 2.45: 4 Bond restraints: 22904 Sorted by residual: bond pdb=" C1 7OC D 907 " pdb=" C3 7OC D 907 " ideal model delta sigma weight residual 1.521 2.451 -0.930 2.00e-02 2.50e+03 2.16e+03 bond pdb=" C1 7OC B 907 " pdb=" C3 7OC B 907 " ideal model delta sigma weight residual 1.521 2.450 -0.929 2.00e-02 2.50e+03 2.16e+03 bond pdb=" C1 7OC C 907 " pdb=" C3 7OC C 907 " ideal model delta sigma weight residual 1.521 2.450 -0.929 2.00e-02 2.50e+03 2.16e+03 bond pdb=" C1 7OC A 907 " pdb=" C3 7OC A 907 " ideal model delta sigma weight residual 1.521 2.450 -0.929 2.00e-02 2.50e+03 2.16e+03 bond pdb=" C8 657 A 905 " pdb=" S1 657 A 905 " ideal model delta sigma weight residual 1.765 1.548 0.217 2.00e-02 2.50e+03 1.18e+02 ... (remaining 22899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.74: 30928 14.74 - 29.49: 16 29.49 - 44.23: 4 44.23 - 58.97: 0 58.97 - 73.72: 4 Bond angle restraints: 30952 Sorted by residual: angle pdb=" C2 7OC D 907 " pdb=" C1 7OC D 907 " pdb=" C3 7OC D 907 " ideal model delta sigma weight residual 109.45 35.73 73.72 3.00e+00 1.11e-01 6.04e+02 angle pdb=" C2 7OC B 907 " pdb=" C1 7OC B 907 " pdb=" C3 7OC B 907 " ideal model delta sigma weight residual 109.45 35.74 73.71 3.00e+00 1.11e-01 6.04e+02 angle pdb=" C2 7OC C 907 " pdb=" C1 7OC C 907 " pdb=" C3 7OC C 907 " ideal model delta sigma weight residual 109.45 35.74 73.71 3.00e+00 1.11e-01 6.04e+02 angle pdb=" C2 7OC A 907 " pdb=" C1 7OC A 907 " pdb=" C3 7OC A 907 " ideal model delta sigma weight residual 109.45 35.75 73.70 3.00e+00 1.11e-01 6.04e+02 angle pdb=" C1 7OC C 907 " pdb=" C3 7OC C 907 " pdb=" O3 7OC C 907 " ideal model delta sigma weight residual 106.89 145.04 -38.15 3.00e+00 1.11e-01 1.62e+02 ... (remaining 30947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 13422 35.69 - 71.37: 230 71.37 - 107.06: 32 107.06 - 142.74: 8 142.74 - 178.43: 8 Dihedral angle restraints: 13700 sinusoidal: 5824 harmonic: 7876 Sorted by residual: dihedral pdb=" C2 7OC D 907 " pdb=" C1 7OC D 907 " pdb=" C3 7OC D 907 " pdb=" O3 7OC D 907 " ideal model delta sinusoidal sigma weight residual -176.68 1.75 -178.43 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C2 7OC B 907 " pdb=" C1 7OC B 907 " pdb=" C3 7OC B 907 " pdb=" O3 7OC B 907 " ideal model delta sinusoidal sigma weight residual -176.68 1.75 -178.43 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C2 7OC A 907 " pdb=" C1 7OC A 907 " pdb=" C3 7OC A 907 " pdb=" O3 7OC A 907 " ideal model delta sinusoidal sigma weight residual -176.68 1.75 -178.43 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2970 0.056 - 0.113: 386 0.113 - 0.169: 48 0.169 - 0.226: 20 0.226 - 0.282: 20 Chirality restraints: 3444 Sorted by residual: chirality pdb=" CA ILE B 631 " pdb=" N ILE B 631 " pdb=" C ILE B 631 " pdb=" CB ILE B 631 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ILE D 631 " pdb=" N ILE D 631 " pdb=" C ILE D 631 " pdb=" CB ILE D 631 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ILE C 631 " pdb=" N ILE C 631 " pdb=" C ILE C 631 " pdb=" CB ILE C 631 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 3441 not shown) Planarity restraints: 3796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 7OC A 907 " 0.200 2.00e-02 2.50e+03 1.82e-01 3.31e+02 pdb=" C20 7OC A 907 " -0.239 2.00e-02 2.50e+03 pdb=" C21 7OC A 907 " -0.111 2.00e-02 2.50e+03 pdb=" C22 7OC A 907 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 7OC B 907 " 0.200 2.00e-02 2.50e+03 1.82e-01 3.31e+02 pdb=" C20 7OC B 907 " -0.240 2.00e-02 2.50e+03 pdb=" C21 7OC B 907 " -0.111 2.00e-02 2.50e+03 pdb=" C22 7OC B 907 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 7OC D 907 " 0.200 2.00e-02 2.50e+03 1.82e-01 3.30e+02 pdb=" C20 7OC D 907 " -0.239 2.00e-02 2.50e+03 pdb=" C21 7OC D 907 " -0.111 2.00e-02 2.50e+03 pdb=" C22 7OC D 907 " 0.150 2.00e-02 2.50e+03 ... (remaining 3793 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5385 2.80 - 3.33: 22314 3.33 - 3.85: 37788 3.85 - 4.38: 44943 4.38 - 4.90: 75877 Nonbonded interactions: 186307 Sorted by model distance: nonbonded pdb=" OG1 THR D 140 " pdb=" OD1 ASP D 142 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR C 140 " pdb=" OD1 ASP C 142 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR A 140 " pdb=" OD1 ASP A 142 " model vdw 2.276 3.040 nonbonded pdb=" O TYR A 430 " pdb=" ND2 ASN A 436 " model vdw 2.349 3.120 ... (remaining 186302 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.370 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: 0.400 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 24.380 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 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 : 0.016 0.930 22924 Z= 0.822 Angle : 1.355 73.718 30972 Z= 0.523 Chirality : 0.046 0.282 3444 Planarity : 0.007 0.182 3796 Dihedral : 14.739 178.426 8560 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.84 % Allowed : 5.22 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.16), residues: 2612 helix: 2.24 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.41 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 260 TYR 0.019 0.001 TYR B 524 PHE 0.019 0.002 PHE B 341 TRP 0.013 0.002 TRP D 639 HIS 0.004 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.01617 / 0.82 (22904) covalent geometry : angle 1.35461 / 0.52 (30952) SS BOND : bond 0.00894 / 0.45 ( 4) SS BOND : angle 0.70906 / 0.42 ( 8) hydrogen bonds : bond 0.11745 / 7.88 ( 1480) hydrogen bonds : angle 4.66598 / 3.37 ( 4308) metal coordination : bond 0.01839 / 1.84 ( 16) metal coordination : angle 2.30450 / 1.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 462 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASN cc_start: 0.8487 (t0) cc_final: 0.8134 (t0) REVERT: A 42 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8558 (mttm) REVERT: A 59 TYR cc_start: 0.8041 (m-80) cc_final: 0.7797 (m-80) REVERT: A 182 VAL cc_start: 0.7772 (m) cc_final: 0.7219 (t) REVERT: A 232 LYS cc_start: 0.8274 (mttp) cc_final: 0.8047 (mptt) REVERT: A 335 MET cc_start: 0.8314 (mmt) cc_final: 0.8045 (mmm) REVERT: A 653 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7861 (pm20) REVERT: B 38 ASN cc_start: 0.8528 (t0) cc_final: 0.8187 (t0) REVERT: B 42 LYS cc_start: 0.8881 (mtmt) cc_final: 0.8586 (mttm) REVERT: B 59 TYR cc_start: 0.8029 (m-80) cc_final: 0.7762 (m-80) REVERT: B 79 GLU cc_start: 0.8495 (tt0) cc_final: 0.8289 (mm-30) REVERT: B 182 VAL cc_start: 0.7734 (m) cc_final: 0.7162 (t) REVERT: B 232 LYS cc_start: 0.8276 (mttp) cc_final: 0.8050 (mptt) REVERT: B 335 MET cc_start: 0.8318 (mmt) cc_final: 0.8052 (mmm) REVERT: B 653 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7863 (pm20) REVERT: C 38 ASN cc_start: 0.8487 (t0) cc_final: 0.7921 (t0) REVERT: C 42 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8456 (mttm) REVERT: C 59 TYR cc_start: 0.8049 (m-80) cc_final: 0.7772 (m-80) REVERT: C 79 GLU cc_start: 0.8493 (tt0) cc_final: 0.8293 (mm-30) REVERT: C 182 VAL cc_start: 0.7759 (m) cc_final: 0.7197 (t) REVERT: C 232 LYS cc_start: 0.8276 (mttp) cc_final: 0.8049 (mptt) REVERT: C 335 MET cc_start: 0.8318 (mmt) cc_final: 0.8046 (mmm) REVERT: C 510 LEU cc_start: 0.8589 (mt) cc_final: 0.8386 (tt) REVERT: C 653 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7858 (pm20) REVERT: D 38 ASN cc_start: 0.8499 (t0) cc_final: 0.8143 (t0) REVERT: D 42 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8568 (mttm) REVERT: D 59 TYR cc_start: 0.8039 (m-80) cc_final: 0.7768 (m-80) REVERT: D 79 GLU cc_start: 0.8491 (tt0) cc_final: 0.8291 (mm-30) REVERT: D 182 VAL cc_start: 0.7771 (m) cc_final: 0.7209 (t) REVERT: D 232 LYS cc_start: 0.8277 (mttp) cc_final: 0.8050 (mptt) REVERT: D 335 MET cc_start: 0.8314 (mmt) cc_final: 0.8046 (mmm) REVERT: D 653 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7862 (pm20) outliers start: 20 outliers final: 8 residues processed: 474 average time/residue: 0.6976 time to fit residues: 372.9373 Evaluate side-chains 265 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 257 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 429 GLU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 431 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN A 552 ASN A 629 GLN A 731 ASN B 304 GLN B 552 ASN B 629 GLN B 731 ASN C 304 GLN C 552 ASN C 629 GLN C 731 ASN D 304 GLN D 552 ASN D 629 GLN D 731 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.110349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077397 restraints weight = 30101.765| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.97 r_work: 0.2790 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22924 Z= 0.141 Angle : 0.525 6.229 30972 Z= 0.262 Chirality : 0.036 0.160 3444 Planarity : 0.004 0.032 3796 Dihedral : 14.859 177.297 3340 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.94 % Allowed : 10.40 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.15 (0.16), residues: 2612 helix: 2.61 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : 0.48 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 170 TYR 0.014 0.001 TYR B 524 PHE 0.018 0.001 PHE B 341 TRP 0.016 0.001 TRP D 315 HIS 0.004 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (22904) covalent geometry : angle 0.52159 / 0.26 (30952) SS BOND : bond 0.00154 / 0.08 ( 4) SS BOND : angle 0.48790 / 0.28 ( 8) hydrogen bonds : bond 0.04332 / 2.92 ( 1480) hydrogen bonds : angle 3.88020 / 2.82 ( 4308) metal coordination : bond 0.00877 / 0.78 ( 16) metal coordination : angle 3.19295 / 1.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6989 (pp30) REVERT: A 38 ASN cc_start: 0.8466 (t0) cc_final: 0.8094 (t0) REVERT: A 42 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8439 (mttm) REVERT: A 113 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8479 (mt-10) REVERT: A 335 MET cc_start: 0.8299 (mmt) cc_final: 0.8050 (mmm) REVERT: A 521 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8145 (mp) REVERT: A 551 ASN cc_start: 0.8427 (t0) cc_final: 0.8116 (t0) REVERT: A 653 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7787 (pm20) REVERT: B 21 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.6778 (pp30) REVERT: B 38 ASN cc_start: 0.8492 (t0) cc_final: 0.8170 (t0) REVERT: B 42 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8440 (mttm) REVERT: B 79 GLU cc_start: 0.8559 (tt0) cc_final: 0.8114 (mm-30) REVERT: B 113 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8475 (mt-10) REVERT: B 232 LYS cc_start: 0.8347 (mttp) cc_final: 0.8123 (mptt) REVERT: B 335 MET cc_start: 0.8287 (mmt) cc_final: 0.8031 (mmm) REVERT: B 521 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8146 (mp) REVERT: B 551 ASN cc_start: 0.8420 (t0) cc_final: 0.8118 (t0) REVERT: B 653 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7847 (pm20) REVERT: C 21 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6769 (pp30) REVERT: C 38 ASN cc_start: 0.8458 (t0) cc_final: 0.8083 (t0) REVERT: C 42 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8439 (mttm) REVERT: C 79 GLU cc_start: 0.8576 (tt0) cc_final: 0.8131 (mm-30) REVERT: C 113 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8469 (mt-10) REVERT: C 232 LYS cc_start: 0.8350 (mttp) cc_final: 0.8124 (mptt) REVERT: C 335 MET cc_start: 0.8292 (mmt) cc_final: 0.8038 (mmm) REVERT: C 521 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8145 (mp) REVERT: C 551 ASN cc_start: 0.8410 (t0) cc_final: 0.8102 (t0) REVERT: C 623 MET cc_start: 0.8965 (mtp) cc_final: 0.8750 (mtm) REVERT: C 653 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7788 (pm20) REVERT: D 21 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6741 (pp30) REVERT: D 38 ASN cc_start: 0.8475 (t0) cc_final: 0.8152 (t0) REVERT: D 42 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8453 (mttm) REVERT: D 79 GLU cc_start: 0.8580 (tt0) cc_final: 0.8122 (mm-30) REVERT: D 113 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8493 (mt-10) REVERT: D 232 LYS cc_start: 0.8344 (mttp) cc_final: 0.8115 (mptt) REVERT: D 335 MET cc_start: 0.8285 (mmt) cc_final: 0.8029 (mmm) REVERT: D 521 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8136 (mp) REVERT: D 551 ASN cc_start: 0.8419 (t0) cc_final: 0.8115 (t0) REVERT: D 653 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7836 (pm20) outliers start: 46 outliers final: 10 residues processed: 304 average time/residue: 0.6702 time to fit residues: 231.9254 Evaluate side-chains 273 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 591 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 241 optimal weight: 0.8980 chunk 119 optimal weight: 0.0370 chunk 257 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 234 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 GLN A 731 ASN B 629 GLN B 731 ASN C 629 GLN C 731 ASN D 629 GLN D 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.078119 restraints weight = 30083.426| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.98 r_work: 0.2803 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22924 Z= 0.110 Angle : 0.457 6.158 30972 Z= 0.233 Chirality : 0.035 0.153 3444 Planarity : 0.003 0.039 3796 Dihedral : 13.126 173.266 3320 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.47 % Allowed : 12.33 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.27 (0.16), residues: 2612 helix: 2.72 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.41 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 170 TYR 0.015 0.001 TYR B 524 PHE 0.017 0.001 PHE A 341 TRP 0.014 0.001 TRP C 315 HIS 0.003 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (22904) covalent geometry : angle 0.45424 / 0.23 (30952) SS BOND : bond 0.00116 / 0.06 ( 4) SS BOND : angle 0.36246 / 0.23 ( 8) hydrogen bonds : bond 0.03945 / 2.66 ( 1480) hydrogen bonds : angle 3.63654 / 2.65 ( 4308) metal coordination : bond 0.00501 / 0.33 ( 16) metal coordination : angle 2.67538 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6691 (pp30) REVERT: A 38 ASN cc_start: 0.8473 (t0) cc_final: 0.7962 (t0) REVERT: A 42 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8330 (mttm) REVERT: A 332 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8472 (mp) REVERT: A 335 MET cc_start: 0.8297 (mmt) cc_final: 0.7973 (mmm) REVERT: A 551 ASN cc_start: 0.8418 (t0) cc_final: 0.8078 (t0) REVERT: A 616 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9052 (mp) REVERT: A 623 MET cc_start: 0.9015 (mtp) cc_final: 0.8741 (mtm) REVERT: A 653 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7764 (pm20) REVERT: B 21 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6732 (pp30) REVERT: B 38 ASN cc_start: 0.8479 (t0) cc_final: 0.7973 (t0) REVERT: B 41 GLU cc_start: 0.8226 (tp30) cc_final: 0.7656 (tp30) REVERT: B 42 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8331 (mttm) REVERT: B 79 GLU cc_start: 0.8536 (tt0) cc_final: 0.8149 (mm-30) REVERT: B 332 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B 335 MET cc_start: 0.8282 (mmt) cc_final: 0.7957 (mmm) REVERT: B 551 ASN cc_start: 0.8406 (t0) cc_final: 0.8072 (t0) REVERT: B 616 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9085 (mp) REVERT: B 623 MET cc_start: 0.9013 (mtp) cc_final: 0.8733 (mtm) REVERT: B 653 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7769 (pm20) REVERT: C 21 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7074 (pp30) REVERT: C 38 ASN cc_start: 0.8476 (t0) cc_final: 0.7970 (t0) REVERT: C 42 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8331 (mttm) REVERT: C 79 GLU cc_start: 0.8559 (tt0) cc_final: 0.8162 (mm-30) REVERT: C 332 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8484 (mp) REVERT: C 335 MET cc_start: 0.8294 (mmt) cc_final: 0.7971 (mmm) REVERT: C 551 ASN cc_start: 0.8402 (t0) cc_final: 0.8079 (t0) REVERT: C 616 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9086 (mp) REVERT: C 623 MET cc_start: 0.8922 (mtp) cc_final: 0.8719 (mtm) REVERT: C 653 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7759 (pm20) REVERT: D 21 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6684 (pp30) REVERT: D 38 ASN cc_start: 0.8476 (t0) cc_final: 0.7968 (t0) REVERT: D 41 GLU cc_start: 0.8226 (tp30) cc_final: 0.7651 (tp30) REVERT: D 42 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8328 (mttm) REVERT: D 79 GLU cc_start: 0.8571 (tt0) cc_final: 0.8118 (mm-30) REVERT: D 332 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8465 (mp) REVERT: D 335 MET cc_start: 0.8306 (mmt) cc_final: 0.7980 (mmm) REVERT: D 551 ASN cc_start: 0.8385 (t0) cc_final: 0.8051 (t0) REVERT: D 616 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9084 (mp) REVERT: D 623 MET cc_start: 0.9004 (mtp) cc_final: 0.8725 (mtm) REVERT: D 653 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7759 (pm20) outliers start: 35 outliers final: 14 residues processed: 309 average time/residue: 0.6807 time to fit residues: 239.1572 Evaluate side-chains 281 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 591 LYS Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 616 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 145 optimal weight: 0.0020 chunk 5 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 GLN A 731 ASN A 742 ASN B 629 GLN B 731 ASN B 742 ASN C 629 GLN C 731 ASN C 742 ASN D 629 GLN D 731 ASN D 742 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.077578 restraints weight = 29946.852| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.96 r_work: 0.2793 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22924 Z= 0.119 Angle : 0.458 6.237 30972 Z= 0.233 Chirality : 0.035 0.153 3444 Planarity : 0.003 0.038 3796 Dihedral : 12.872 176.489 3320 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.10 % Allowed : 12.58 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.28 (0.16), residues: 2612 helix: 2.75 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.38 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 170 TYR 0.015 0.001 TYR C 524 PHE 0.017 0.001 PHE A 341 TRP 0.014 0.001 TRP A 315 HIS 0.002 0.000 HIS C 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (22904) covalent geometry : angle 0.45737 / 0.23 (30952) SS BOND : bond 0.00134 / 0.07 ( 4) SS BOND : angle 0.40121 / 0.24 ( 8) hydrogen bonds : bond 0.03964 / 2.68 ( 1480) hydrogen bonds : angle 3.57161 / 2.60 ( 4308) metal coordination : bond 0.00300 / 0.26 ( 16) metal coordination : angle 1.45845 / 1.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6685 (pp30) REVERT: A 38 ASN cc_start: 0.8484 (t0) cc_final: 0.7968 (t0) REVERT: A 42 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8330 (mttm) REVERT: A 180 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8518 (mp0) REVERT: A 335 MET cc_start: 0.8264 (mmt) cc_final: 0.7899 (mtm) REVERT: A 623 MET cc_start: 0.8993 (mtp) cc_final: 0.8754 (mtm) REVERT: B 21 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6719 (pp30) REVERT: B 38 ASN cc_start: 0.8504 (t0) cc_final: 0.8071 (t0) REVERT: B 41 GLU cc_start: 0.8235 (tp30) cc_final: 0.7658 (tp30) REVERT: B 42 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8328 (mttm) REVERT: B 79 GLU cc_start: 0.8478 (tt0) cc_final: 0.8123 (mm-30) REVERT: B 180 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8503 (mp0) REVERT: B 335 MET cc_start: 0.8248 (mmt) cc_final: 0.7884 (mtm) REVERT: B 623 MET cc_start: 0.8988 (mtp) cc_final: 0.8747 (mtm) REVERT: C 21 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6736 (pp30) REVERT: C 38 ASN cc_start: 0.8489 (t0) cc_final: 0.7977 (t0) REVERT: C 42 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8331 (mttm) REVERT: C 79 GLU cc_start: 0.8550 (tt0) cc_final: 0.8137 (mm-30) REVERT: C 180 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8513 (mp0) REVERT: C 335 MET cc_start: 0.8259 (mmt) cc_final: 0.8012 (mmm) REVERT: D 21 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6673 (pp30) REVERT: D 38 ASN cc_start: 0.8497 (t0) cc_final: 0.8061 (t0) REVERT: D 42 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8317 (mttm) REVERT: D 79 GLU cc_start: 0.8508 (tt0) cc_final: 0.8131 (mm-30) REVERT: D 180 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8502 (mp0) REVERT: D 335 MET cc_start: 0.8274 (mmt) cc_final: 0.7910 (mtm) REVERT: D 623 MET cc_start: 0.8983 (mtp) cc_final: 0.8744 (mtm) outliers start: 50 outliers final: 18 residues processed: 313 average time/residue: 0.6719 time to fit residues: 239.4274 Evaluate side-chains 273 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 163 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 629 GLN A 731 ASN B 163 GLN B 629 GLN B 731 ASN C 163 GLN C 629 GLN C 731 ASN D 163 GLN D 629 GLN D 731 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.110840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.078119 restraints weight = 29842.686| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.96 r_work: 0.2803 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22924 Z= 0.108 Angle : 0.446 6.386 30972 Z= 0.227 Chirality : 0.035 0.150 3444 Planarity : 0.003 0.039 3796 Dihedral : 12.428 175.086 3320 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.06 % Allowed : 13.55 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.31 (0.16), residues: 2612 helix: 2.77 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.35 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 170 TYR 0.014 0.001 TYR B 524 PHE 0.017 0.001 PHE A 341 TRP 0.013 0.001 TRP C 315 HIS 0.001 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (22904) covalent geometry : angle 0.44497 / 0.23 (30952) SS BOND : bond 0.00114 / 0.06 ( 4) SS BOND : angle 0.34339 / 0.20 ( 8) hydrogen bonds : bond 0.03818 / 2.59 ( 1480) hydrogen bonds : angle 3.52330 / 2.56 ( 4308) metal coordination : bond 0.00242 / 0.20 ( 16) metal coordination : angle 1.42013 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6945 (pp30) REVERT: A 38 ASN cc_start: 0.8487 (t0) cc_final: 0.8034 (t0) REVERT: A 42 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8317 (mttm) REVERT: A 180 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8508 (mp0) REVERT: A 623 MET cc_start: 0.8964 (mtp) cc_final: 0.8734 (mtm) REVERT: B 21 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6679 (pp30) REVERT: B 38 ASN cc_start: 0.8497 (t0) cc_final: 0.8059 (t0) REVERT: B 42 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8338 (mttm) REVERT: B 79 GLU cc_start: 0.8470 (tt0) cc_final: 0.8109 (mm-30) REVERT: B 180 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8500 (mp0) REVERT: B 335 MET cc_start: 0.8241 (mmt) cc_final: 0.7913 (mtm) REVERT: B 623 MET cc_start: 0.8963 (mtp) cc_final: 0.8730 (mtm) REVERT: C 21 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6686 (pp30) REVERT: C 38 ASN cc_start: 0.8488 (t0) cc_final: 0.7983 (t0) REVERT: C 42 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8323 (mttm) REVERT: C 79 GLU cc_start: 0.8546 (tt0) cc_final: 0.8132 (mm-30) REVERT: C 180 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8507 (mp0) REVERT: D 21 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6979 (pp30) REVERT: D 38 ASN cc_start: 0.8490 (t0) cc_final: 0.8051 (t0) REVERT: D 42 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8335 (mttm) REVERT: D 79 GLU cc_start: 0.8494 (tt0) cc_final: 0.8125 (mm-30) REVERT: D 180 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8504 (mp0) REVERT: D 335 MET cc_start: 0.8259 (mmt) cc_final: 0.7932 (mtm) REVERT: D 623 MET cc_start: 0.8959 (mtp) cc_final: 0.8729 (mtm) outliers start: 49 outliers final: 18 residues processed: 295 average time/residue: 0.6110 time to fit residues: 207.5357 Evaluate side-chains 264 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 143 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 GLN A 731 ASN B 629 GLN B 731 ASN C 629 GLN C 731 ASN D 629 GLN D 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.109618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.076828 restraints weight = 29991.478| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.95 r_work: 0.2777 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22924 Z= 0.137 Angle : 0.468 7.051 30972 Z= 0.239 Chirality : 0.035 0.151 3444 Planarity : 0.003 0.041 3796 Dihedral : 12.513 179.737 3320 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.15 % Allowed : 13.55 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.25 (0.16), residues: 2612 helix: 2.72 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.37 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 170 TYR 0.017 0.001 TYR B 524 PHE 0.017 0.001 PHE A 341 TRP 0.014 0.001 TRP C 315 HIS 0.002 0.001 HIS C 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (22904) covalent geometry : angle 0.46709 / 0.24 (30952) SS BOND : bond 0.00150 / 0.07 ( 4) SS BOND : angle 0.37327 / 0.21 ( 8) hydrogen bonds : bond 0.04130 / 2.80 ( 1480) hydrogen bonds : angle 3.57691 / 2.60 ( 4308) metal coordination : bond 0.00243 / 0.19 ( 16) metal coordination : angle 1.33477 / 0.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7028 (pp30) REVERT: A 38 ASN cc_start: 0.8522 (t0) cc_final: 0.8074 (t0) REVERT: A 42 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8354 (mttm) REVERT: A 180 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8514 (mp0) REVERT: A 552 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8564 (t0) REVERT: A 623 MET cc_start: 0.8992 (mtp) cc_final: 0.8775 (mtm) REVERT: B 21 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6755 (pp30) REVERT: B 38 ASN cc_start: 0.8502 (t0) cc_final: 0.8070 (t0) REVERT: B 42 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8313 (mttm) REVERT: B 79 GLU cc_start: 0.8479 (tt0) cc_final: 0.8131 (mm-30) REVERT: B 180 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8523 (mp0) REVERT: B 552 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8535 (t0) REVERT: B 623 MET cc_start: 0.8973 (mtp) cc_final: 0.8748 (mtm) REVERT: C 21 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6769 (pp30) REVERT: C 38 ASN cc_start: 0.8505 (t0) cc_final: 0.8070 (t0) REVERT: C 42 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8346 (mttm) REVERT: C 79 GLU cc_start: 0.8508 (tt0) cc_final: 0.8077 (mm-30) REVERT: C 180 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8522 (mp0) REVERT: C 552 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8548 (t0) REVERT: D 21 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7020 (pp30) REVERT: D 38 ASN cc_start: 0.8514 (t0) cc_final: 0.8067 (t0) REVERT: D 42 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8303 (mttm) REVERT: D 79 GLU cc_start: 0.8483 (tt0) cc_final: 0.8112 (mm-30) REVERT: D 180 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8523 (mp0) REVERT: D 552 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8549 (t0) REVERT: D 623 MET cc_start: 0.8963 (mtp) cc_final: 0.8739 (mtm) outliers start: 51 outliers final: 14 residues processed: 300 average time/residue: 0.6268 time to fit residues: 215.9497 Evaluate side-chains 270 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 552 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 GLN A 731 ASN B 629 GLN B 731 ASN C 629 GLN C 731 ASN D 629 GLN D 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.109782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.078779 restraints weight = 30271.786| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.84 r_work: 0.2841 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22924 Z= 0.138 Angle : 0.481 8.309 30972 Z= 0.244 Chirality : 0.036 0.151 3444 Planarity : 0.003 0.041 3796 Dihedral : 12.364 178.507 3320 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.85 % Allowed : 14.10 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.26 (0.16), residues: 2612 helix: 2.71 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.47 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 170 TYR 0.017 0.001 TYR A 524 PHE 0.017 0.002 PHE B 341 TRP 0.014 0.001 TRP D 315 HIS 0.003 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (22904) covalent geometry : angle 0.48000 / 0.24 (30952) SS BOND : bond 0.00145 / 0.07 ( 4) SS BOND : angle 0.38917 / 0.22 ( 8) hydrogen bonds : bond 0.04133 / 2.80 ( 1480) hydrogen bonds : angle 3.57413 / 2.60 ( 4308) metal coordination : bond 0.00254 / 0.23 ( 16) metal coordination : angle 1.26632 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7096 (pp30) REVERT: A 38 ASN cc_start: 0.8629 (t0) cc_final: 0.8217 (t0) REVERT: A 42 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8470 (mttm) REVERT: A 180 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8559 (mp0) REVERT: A 623 MET cc_start: 0.9028 (mtp) cc_final: 0.8825 (mtm) REVERT: B 21 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.6783 (pp30) REVERT: B 38 ASN cc_start: 0.8617 (t0) cc_final: 0.8208 (t0) REVERT: B 42 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8454 (mttm) REVERT: B 79 GLU cc_start: 0.8505 (tt0) cc_final: 0.8283 (mm-30) REVERT: B 552 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8551 (t0) REVERT: B 623 MET cc_start: 0.9011 (mtp) cc_final: 0.8799 (mtm) REVERT: C 21 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6782 (pp30) REVERT: C 38 ASN cc_start: 0.8619 (t0) cc_final: 0.8204 (t0) REVERT: C 42 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8461 (mttm) REVERT: C 79 GLU cc_start: 0.8496 (tt0) cc_final: 0.8256 (mm-30) REVERT: C 552 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8566 (t0) REVERT: D 21 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7093 (pp30) REVERT: D 38 ASN cc_start: 0.8633 (t0) cc_final: 0.8218 (t0) REVERT: D 42 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8451 (mttm) REVERT: D 79 GLU cc_start: 0.8498 (tt0) cc_final: 0.8288 (mm-30) REVERT: D 623 MET cc_start: 0.9032 (mtp) cc_final: 0.8829 (mtm) outliers start: 44 outliers final: 15 residues processed: 299 average time/residue: 0.6042 time to fit residues: 207.0607 Evaluate side-chains 272 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 260 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A 731 ASN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN B 731 ASN C 629 GLN C 731 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN D 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.108247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.076715 restraints weight = 30276.814| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.87 r_work: 0.2806 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9211 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22924 Z= 0.228 Angle : 0.557 9.595 30972 Z= 0.283 Chirality : 0.039 0.227 3444 Planarity : 0.004 0.039 3796 Dihedral : 12.856 172.932 3320 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.81 % Allowed : 14.35 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.00 (0.16), residues: 2612 helix: 2.53 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.32 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.021 0.002 TYR B 524 PHE 0.018 0.002 PHE B 580 TRP 0.016 0.002 TRP D 315 HIS 0.004 0.001 HIS A 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (22904) covalent geometry : angle 0.55510 / 0.28 (30952) SS BOND : bond 0.00136 / 0.07 ( 4) SS BOND : angle 0.48589 / 0.28 ( 8) hydrogen bonds : bond 0.04820 / 3.27 ( 1480) hydrogen bonds : angle 3.73735 / 2.71 ( 4308) metal coordination : bond 0.00513 / 0.36 ( 16) metal coordination : angle 2.22740 / 1.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7152 (pp30) REVERT: A 38 ASN cc_start: 0.8584 (t0) cc_final: 0.8108 (t0) REVERT: A 42 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8416 (mttm) REVERT: A 186 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: A 232 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8508 (mppt) REVERT: A 623 MET cc_start: 0.9091 (mtp) cc_final: 0.8856 (mtm) REVERT: B 21 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.6888 (pp30) REVERT: B 38 ASN cc_start: 0.8595 (t0) cc_final: 0.8348 (t0) REVERT: B 42 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8593 (mttm) REVERT: B 79 GLU cc_start: 0.8516 (tt0) cc_final: 0.8268 (mm-30) REVERT: B 623 MET cc_start: 0.9092 (mtp) cc_final: 0.8853 (mtm) REVERT: C 21 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.6883 (pp30) REVERT: C 38 ASN cc_start: 0.8582 (t0) cc_final: 0.8185 (t0) REVERT: C 42 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8422 (mttm) REVERT: C 79 GLU cc_start: 0.8518 (tt0) cc_final: 0.8252 (mm-30) REVERT: C 186 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: D 21 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.6848 (pp30) REVERT: D 38 ASN cc_start: 0.8610 (t0) cc_final: 0.8361 (t0) REVERT: D 42 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8588 (mttm) REVERT: D 79 GLU cc_start: 0.8510 (tt0) cc_final: 0.8288 (mm-30) REVERT: D 623 MET cc_start: 0.9085 (mtp) cc_final: 0.8880 (mtm) outliers start: 43 outliers final: 12 residues processed: 298 average time/residue: 0.5790 time to fit residues: 197.1711 Evaluate side-chains 272 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 217 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 235 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 GLN A 731 ASN B 629 GLN B 731 ASN C 629 GLN C 731 ASN D 629 GLN D 731 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.079586 restraints weight = 30168.167| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.82 r_work: 0.2858 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22924 Z= 0.117 Angle : 0.491 9.759 30972 Z= 0.250 Chirality : 0.036 0.212 3444 Planarity : 0.003 0.027 3796 Dihedral : 12.151 179.154 3320 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.35 % Allowed : 14.90 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.17 (0.16), residues: 2612 helix: 2.65 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.43 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 353 TYR 0.015 0.001 TYR B 524 PHE 0.017 0.001 PHE C 341 TRP 0.014 0.001 TRP A 315 HIS 0.001 0.000 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (22904) covalent geometry : angle 0.49022 / 0.25 (30952) SS BOND : bond 0.00062 / 0.03 ( 4) SS BOND : angle 0.22889 / 0.13 ( 8) hydrogen bonds : bond 0.03900 / 2.65 ( 1480) hydrogen bonds : angle 3.57294 / 2.60 ( 4308) metal coordination : bond 0.00403 / 0.43 ( 16) metal coordination : angle 1.31795 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 282 time to evaluate : 0.855 Fit side-chains REVERT: A 21 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7090 (pp30) REVERT: A 38 ASN cc_start: 0.8587 (t0) cc_final: 0.8068 (t0) REVERT: A 42 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8394 (mttm) REVERT: A 186 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: A 232 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8462 (mppt) REVERT: A 552 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8564 (t0) REVERT: A 623 MET cc_start: 0.9005 (mtp) cc_final: 0.8786 (mtm) REVERT: B 21 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.6874 (pp30) REVERT: B 38 ASN cc_start: 0.8582 (t0) cc_final: 0.8317 (t0) REVERT: B 42 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8565 (mttm) REVERT: B 79 GLU cc_start: 0.8496 (tt0) cc_final: 0.8241 (mm-30) REVERT: B 623 MET cc_start: 0.9003 (mtp) cc_final: 0.8783 (mtm) REVERT: C 21 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6863 (pp30) REVERT: C 38 ASN cc_start: 0.8570 (t0) cc_final: 0.8069 (t0) REVERT: C 42 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8400 (mttm) REVERT: C 79 GLU cc_start: 0.8480 (tt0) cc_final: 0.8200 (mm-30) REVERT: C 186 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: D 21 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7124 (pp30) REVERT: D 38 ASN cc_start: 0.8576 (t0) cc_final: 0.8310 (t0) REVERT: D 42 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8567 (mttm) REVERT: D 79 GLU cc_start: 0.8488 (tt0) cc_final: 0.8241 (mm-30) REVERT: D 552 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8569 (t0) REVERT: D 623 MET cc_start: 0.8997 (mtp) cc_final: 0.8773 (mtm) outliers start: 32 outliers final: 10 residues processed: 308 average time/residue: 0.6266 time to fit residues: 218.9319 Evaluate side-chains 281 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 262 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 552 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 128 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 163 GLN A 629 GLN A 731 ASN B 163 GLN B 629 GLN C 163 GLN C 629 GLN C 731 ASN D 163 GLN D 629 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.109165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.078185 restraints weight = 30139.123| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.82 r_work: 0.2842 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9199 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22924 Z= 0.159 Angle : 0.531 9.876 30972 Z= 0.272 Chirality : 0.037 0.232 3444 Planarity : 0.003 0.028 3796 Dihedral : 12.268 176.809 3320 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.14 % Allowed : 15.32 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.09 (0.16), residues: 2612 helix: 2.60 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.38 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 17 TYR 0.017 0.001 TYR B 524 PHE 0.018 0.001 PHE C 341 TRP 0.015 0.001 TRP B 315 HIS 0.003 0.001 HIS C 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (22904) covalent geometry : angle 0.53065 / 0.27 (30952) SS BOND : bond 0.00142 / 0.07 ( 4) SS BOND : angle 0.32460 / 0.19 ( 8) hydrogen bonds : bond 0.04312 / 2.93 ( 1480) hydrogen bonds : angle 3.64431 / 2.65 ( 4308) metal coordination : bond 0.00463 / 0.34 ( 16) metal coordination : angle 1.63609 / 1.18 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 262 time to evaluate : 0.818 Fit side-chains REVERT: A 21 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7160 (pp30) REVERT: A 38 ASN cc_start: 0.8592 (t0) cc_final: 0.8082 (t0) REVERT: A 42 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8406 (mttm) REVERT: A 180 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8587 (mp0) REVERT: A 232 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8499 (mppt) REVERT: B 21 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.6899 (pp30) REVERT: B 38 ASN cc_start: 0.8595 (t0) cc_final: 0.8342 (t0) REVERT: B 42 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8599 (mttm) REVERT: B 79 GLU cc_start: 0.8503 (tt0) cc_final: 0.8286 (mm-30) REVERT: B 623 MET cc_start: 0.9060 (mtp) cc_final: 0.8858 (mtm) REVERT: C 21 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.6902 (pp30) REVERT: C 38 ASN cc_start: 0.8596 (t0) cc_final: 0.8090 (t0) REVERT: C 42 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8407 (mttm) REVERT: C 79 GLU cc_start: 0.8501 (tt0) cc_final: 0.8277 (mm-30) REVERT: C 335 MET cc_start: 0.8686 (mtp) cc_final: 0.8327 (mtm) REVERT: D 21 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7164 (pp30) REVERT: D 38 ASN cc_start: 0.8610 (t0) cc_final: 0.8355 (t0) REVERT: D 42 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8594 (mttm) REVERT: D 79 GLU cc_start: 0.8491 (tt0) cc_final: 0.8273 (mm-30) REVERT: D 335 MET cc_start: 0.8703 (mtp) cc_final: 0.8333 (mtm) REVERT: D 623 MET cc_start: 0.9060 (mtp) cc_final: 0.8858 (mtm) outliers start: 27 outliers final: 14 residues processed: 287 average time/residue: 0.6592 time to fit residues: 214.9200 Evaluate side-chains 277 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 258 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 218 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 231 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 159 optimal weight: 0.0050 chunk 153 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 GLN A 731 ASN B 629 GLN C 629 GLN D 629 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.080237 restraints weight = 30137.769| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.82 r_work: 0.2882 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22924 Z= 0.109 Angle : 0.485 9.488 30972 Z= 0.247 Chirality : 0.035 0.220 3444 Planarity : 0.003 0.028 3796 Dihedral : 11.707 177.926 3320 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.84 % Allowed : 15.74 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 3.22 (0.16), residues: 2612 helix: 2.70 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.39 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 17 TYR 0.014 0.001 TYR A 524 PHE 0.017 0.001 PHE C 341 TRP 0.014 0.001 TRP A 315 HIS 0.001 0.000 HIS B 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (22904) covalent geometry : angle 0.48464 / 0.25 (30952) SS BOND : bond 0.00061 / 0.03 ( 4) SS BOND : angle 0.20571 / 0.12 ( 8) hydrogen bonds : bond 0.03739 / 2.54 ( 1480) hydrogen bonds : angle 3.53398 / 2.57 ( 4308) metal coordination : bond 0.00391 / 0.42 ( 16) metal coordination : angle 0.91812 / 0.61 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9369.65 seconds wall clock time: 160 minutes 5.74 seconds (9605.74 seconds total)