Starting phenix.real_space_refine on Sat Feb 7 04:38:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ef9_47971/02_2026/9ef9_47971_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ef9_47971/02_2026/9ef9_47971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ef9_47971/02_2026/9ef9_47971_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ef9_47971/02_2026/9ef9_47971_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ef9_47971/02_2026/9ef9_47971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ef9_47971/02_2026/9ef9_47971.map" } resolution = 3.6 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= 0.001 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: 5 Type Number sf(0) Gaussians S 130 5.16 5 C 9309 2.51 5 N 2524 2.21 5 O 2880 1.98 5 H 14213 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29056 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 13236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 13236 Classifications: {'peptide': 846} Link IDs: {'PTRANS': 43, 'TRANS': 802} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 13427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 13427 Classifications: {'peptide': 857} Link IDs: {'CIS': 1, 'PTRANS': 42, 'TRANS': 813} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 339 Classifications: {'peptide': 24} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 381 Classifications: {'peptide': 27} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 24} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 337 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "F" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 345 Classifications: {'peptide': 24} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 349 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "H" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 376 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.17, per 1000 atoms: 0.18 Number of scatterers: 29056 At special positions: 0 Unit cell: (156.2, 108.9, 181.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 130 16.00 O 2880 8.00 N 2524 7.00 C 9309 6.00 H 14213 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 512 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 539 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 591 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 618 " distance=2.03 Simple disulfide: pdb=" SG CYS A 622 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 638 " - pdb=" SG CYS A 643 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS A 664 " distance=2.03 Simple disulfide: pdb=" SG CYS A 770 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS A 873 " - pdb=" SG CYS B 873 " distance=2.03 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS A1258 " distance=2.03 Simple disulfide: pdb=" SG CYS A1169 " - pdb=" SG CYS A1188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 454 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 539 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 564 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 591 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 618 " distance=2.03 Simple disulfide: pdb=" SG CYS B 622 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 638 " - pdb=" SG CYS B 643 " distance=2.03 Simple disulfide: pdb=" SG CYS B 647 " - pdb=" SG CYS B 664 " distance=2.03 Simple disulfide: pdb=" SG CYS B 770 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 981 " - pdb=" SG CYS B1258 " distance=2.03 Simple disulfide: pdb=" SG CYS B1169 " - pdb=" SG CYS B1188 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 14 " distance=2.03 Simple disulfide: pdb=" SG CYS C 10 " - pdb=" SG CYS D 6 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS D 18 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 14 " distance=2.03 Simple disulfide: pdb=" SG CYS E 10 " - pdb=" SG CYS F 6 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS F 18 " distance=2.03 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 14 " distance=2.03 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS H 6 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS H 18 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2201 " - " ASN A 356 " " NAG A2202 " - " ASN A 751 " " NAG A2203 " - " ASN A 810 " " NAG A2204 " - " ASN A 824 " " NAG A2205 " - " ASN A 864 " " NAG A2206 " - " ASN A 898 " " NAG A2207 " - " ASN A 946 " " NAG A2208 " - " ASN A1147 " " NAG A2209 " - " ASN A 376 " " NAG B2201 " - " ASN B 356 " " NAG B2202 " - " ASN B 810 " " NAG B2203 " - " ASN B 824 " " NAG B2204 " - " ASN B 864 " " NAG B2205 " - " ASN B 898 " " NAG B2206 " - " ASN B 946 " " NAG B2207 " - " ASN B1147 " " NAG B2208 " - " ASN B 376 " " NAG B2209 " - " ASN B 751 " " NAG B2210 " - " ASN B 839 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 793.1 milliseconds 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3498 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 37 sheets defined 15.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 347 through 355 removed outlier: 3.538A pdb=" N HIS A 350 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.728A pdb=" N ILE A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.802A pdb=" N ARG A 536 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 639 through 642 removed outlier: 3.795A pdb=" N LYS A 642 " --> pdb=" O PRO A 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 639 through 642' Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 684 through 694 removed outlier: 3.522A pdb=" N ALA A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.503A pdb=" N ILE A 774 " --> pdb=" O CYS A 770 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 781 removed outlier: 3.586A pdb=" N LEU A 781 " --> pdb=" O LEU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1044 removed outlier: 3.663A pdb=" N PHE A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1179 removed outlier: 3.562A pdb=" N LEU A1178 " --> pdb=" O PRO A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1268 removed outlier: 3.978A pdb=" N THR A1267 " --> pdb=" O PHE A1264 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 355 Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.513A pdb=" N SER B 487 " --> pdb=" O CYS B 484 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 488 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS B 489 " --> pdb=" O LEU B 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 484 through 489' Processing helix chain 'B' and resid 593 through 598 Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 660 through 662 No H-bonds generated for 'chain 'B' and resid 660 through 662' Processing helix chain 'B' and resid 683 through 694 removed outlier: 4.426A pdb=" N ASP B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 4.454A pdb=" N PHE B 716 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 733 removed outlier: 3.927A pdb=" N ASP B 732 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 775 removed outlier: 3.576A pdb=" N ILE B 774 " --> pdb=" O CYS B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 778 No H-bonds generated for 'chain 'B' and resid 776 through 778' Processing helix chain 'B' and resid 846 through 848 No H-bonds generated for 'chain 'B' and resid 846 through 848' Processing helix chain 'B' and resid 1026 through 1044 Processing helix chain 'B' and resid 1120 through 1124 Processing helix chain 'B' and resid 1175 through 1180 Processing helix chain 'C' and resid 4 through 10 Processing helix chain 'C' and resid 15 through 20 removed outlier: 3.861A pdb=" N LEU C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 15 through 21 Processing helix chain 'F' and resid 7 through 18 Processing helix chain 'G' and resid 4 through 9 Processing helix chain 'G' and resid 15 through 20 Processing helix chain 'H' and resid 6 through 18 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 331 removed outlier: 4.141A pdb=" N MET A 330 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 339 removed outlier: 3.525A pdb=" N VAL A 385 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 342 through 345 removed outlier: 6.730A pdb=" N VAL A 394 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG A 446 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 422 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLU A 448 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR A 424 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 521 through 522 removed outlier: 3.934A pdb=" N LEU A 526 " --> pdb=" O TRP A 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 550 through 555 removed outlier: 4.478A pdb=" N LEU A 551 " --> pdb=" O CYS A 567 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N CYS A 567 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLY A 553 " --> pdb=" O ILE A 565 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AA7, first strand: chain 'A' and resid 601 through 604 Processing sheet with id=AA8, first strand: chain 'A' and resid 612 through 614 Processing sheet with id=AA9, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AB1, first strand: chain 'A' and resid 646 through 648 Processing sheet with id=AB2, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.533A pdb=" N GLY A 760 " --> pdb=" O TYR A 734 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 736 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 807 through 808 removed outlier: 6.510A pdb=" N ALA A 807 " --> pdb=" O GLU A 916 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 811 through 816 removed outlier: 6.827A pdb=" N MET A 822 " --> pdb=" O GLN A 814 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 830 through 831 removed outlier: 6.532A pdb=" N GLU A 830 " --> pdb=" O PHE A 844 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 850 through 859 removed outlier: 3.537A pdb=" N TYR A 901 " --> pdb=" O LYS A 920 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 933 through 939 removed outlier: 4.539A pdb=" N GLU A 934 " --> pdb=" O SER A 950 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 950 " --> pdb=" O GLU A 934 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1127 through 1130 removed outlier: 6.882A pdb=" N GLU A1127 " --> pdb=" O PHE A1140 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE A1140 " --> pdb=" O GLU A1127 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP A1129 " --> pdb=" O GLU A1138 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLU A1138 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 961 " --> pdb=" O CYS A1169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1127 through 1130 removed outlier: 6.882A pdb=" N GLU A1127 " --> pdb=" O PHE A1140 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE A1140 " --> pdb=" O GLU A1127 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP A1129 " --> pdb=" O GLU A1138 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N GLU A1138 " --> pdb=" O LEU A 968 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1208 through 1214 removed outlier: 5.369A pdb=" N ASP A1209 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A1229 " --> pdb=" O ASP A1209 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1255 through 1259 Processing sheet with id=AC3, first strand: chain 'B' and resid 342 through 344 removed outlier: 6.662A pdb=" N MET B 342 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ASP B 367 " --> pdb=" O MET B 342 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE B 344 " --> pdb=" O ASP B 367 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 390 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE B 389 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR B 424 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE B 391 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG B 446 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL B 422 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLU B 448 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR B 424 " --> pdb=" O GLU B 448 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 360 Processing sheet with id=AC5, first strand: chain 'B' and resid 514 through 515 Processing sheet with id=AC6, first strand: chain 'B' and resid 554 through 556 Processing sheet with id=AC7, first strand: chain 'B' and resid 570 through 572 Processing sheet with id=AC8, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AC9, first strand: chain 'B' and resid 612 through 614 Processing sheet with id=AD1, first strand: chain 'B' and resid 626 through 628 Processing sheet with id=AD2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.409A pdb=" N CYS B 647 " --> pdb=" O THR B 668 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 673 through 675 removed outlier: 7.085A pdb=" N LEU B 703 " --> pdb=" O TYR B 737 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU B 739 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 705 " --> pdb=" O LEU B 739 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY B 760 " --> pdb=" O TYR B 734 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 736 " --> pdb=" O GLY B 760 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 811 through 812 Processing sheet with id=AD5, first strand: chain 'B' and resid 878 through 879 removed outlier: 3.738A pdb=" N GLY B 852 " --> pdb=" O MET B 906 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 933 through 939 removed outlier: 5.022A pdb=" N GLU B 934 " --> pdb=" O SER B 950 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER B 950 " --> pdb=" O GLU B 934 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1127 through 1130 removed outlier: 6.776A pdb=" N GLU B1127 " --> pdb=" O PHE B1140 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE B1140 " --> pdb=" O GLU B1127 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASP B1129 " --> pdb=" O GLU B1138 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLU B1138 " --> pdb=" O LEU B 968 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 961 " --> pdb=" O CYS B1169 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1208 through 1214 removed outlier: 5.722A pdb=" N ASP B1209 " --> pdb=" O THR B1229 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B1229 " --> pdb=" O ASP B1209 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1255 through 1260 Processing sheet with id=AE1, first strand: chain 'B' and resid 1255 through 1260 375 hydrogen bonds defined for protein. 927 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: 7.11 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14213 1.03 - 1.23: 71 1.23 - 1.43: 6225 1.43 - 1.62: 8669 1.62 - 1.82: 172 Bond restraints: 29350 Sorted by residual: bond pdb=" N PHE G 2 " pdb=" CA PHE G 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N PHE E 2 " pdb=" CA PHE E 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N SER H 2 " pdb=" CA SER H 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" CG1 ILE B 410 " pdb=" CD1 ILE B 410 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.73e+00 bond pdb=" N PRO A1304 " pdb=" CA PRO A1304 " ideal model delta sigma weight residual 1.465 1.498 -0.033 2.03e-02 2.43e+03 2.60e+00 ... (remaining 29345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 49984 1.21 - 2.41: 2631 2.41 - 3.62: 219 3.62 - 4.82: 46 4.82 - 6.03: 6 Bond angle restraints: 52886 Sorted by residual: angle pdb=" N ASN B 346 " pdb=" CA ASN B 346 " pdb=" CB ASN B 346 " ideal model delta sigma weight residual 114.17 109.50 4.67 1.14e+00 7.69e-01 1.68e+01 angle pdb=" N ALA G 21 " pdb=" CA ALA G 21 " pdb=" C ALA G 21 " ideal model delta sigma weight residual 114.56 109.52 5.04 1.27e+00 6.20e-01 1.58e+01 angle pdb=" N ILE A1206 " pdb=" CA ILE A1206 " pdb=" C ILE A1206 " ideal model delta sigma weight residual 111.62 109.05 2.57 7.90e-01 1.60e+00 1.06e+01 angle pdb=" N ASP B 726 " pdb=" CA ASP B 726 " pdb=" C ASP B 726 " ideal model delta sigma weight residual 112.55 108.17 4.38 1.35e+00 5.49e-01 1.05e+01 angle pdb=" C GLN B 835 " pdb=" N LYS B 836 " pdb=" CA LYS B 836 " ideal model delta sigma weight residual 121.70 127.36 -5.66 1.80e+00 3.09e-01 9.89e+00 ... (remaining 52881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 12873 18.01 - 36.03: 1014 36.03 - 54.04: 306 54.04 - 72.06: 75 72.06 - 90.07: 23 Dihedral angle restraints: 14291 sinusoidal: 7989 harmonic: 6302 Sorted by residual: dihedral pdb=" CB CYS B 531 " pdb=" SG CYS B 531 " pdb=" SG CYS B 535 " pdb=" CB CYS B 535 " ideal model delta sinusoidal sigma weight residual -86.00 -176.07 90.07 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS G 10 " pdb=" SG CYS G 10 " pdb=" SG CYS H 6 " pdb=" CB CYS H 6 " ideal model delta sinusoidal sigma weight residual -86.00 -173.00 87.00 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS E 10 " pdb=" SG CYS E 10 " pdb=" SG CYS F 6 " pdb=" CB CYS F 6 " ideal model delta sinusoidal sigma weight residual -86.00 -162.45 76.45 1 1.00e+01 1.00e-02 7.35e+01 ... (remaining 14288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2092 0.083 - 0.166: 218 0.166 - 0.249: 6 0.249 - 0.332: 2 0.332 - 0.415: 1 Chirality restraints: 2319 Sorted by residual: chirality pdb=" C1 NAG A2207 " pdb=" ND2 ASN A 946 " pdb=" C2 NAG A2207 " pdb=" O5 NAG A2207 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" C1 NAG B2203 " pdb=" ND2 ASN B 824 " pdb=" C2 NAG B2203 " pdb=" O5 NAG B2203 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C1 NAG A2204 " pdb=" ND2 ASN A 824 " pdb=" C2 NAG A2204 " pdb=" O5 NAG A2204 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2316 not shown) Planarity restraints: 4398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B1303 " -0.024 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C GLU B1303 " 0.081 2.00e-02 2.50e+03 pdb=" O GLU B1303 " -0.030 2.00e-02 2.50e+03 pdb=" N PRO B1304 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1303 " 0.023 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C GLU A1303 " -0.077 2.00e-02 2.50e+03 pdb=" O GLU A1303 " 0.029 2.00e-02 2.50e+03 pdb=" N PRO A1304 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1249 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO A1250 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A1250 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1250 " 0.036 5.00e-02 4.00e+02 ... (remaining 4395 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 901 2.12 - 2.74: 51902 2.74 - 3.36: 80820 3.36 - 3.98: 101887 3.98 - 4.60: 158440 Nonbonded interactions: 393950 Sorted by model distance: nonbonded pdb=" OD1 ASP A 541 " pdb=" H THR A 544 " model vdw 1.501 2.450 nonbonded pdb=" OD1 ASP B 541 " pdb=" H THR B 544 " model vdw 1.520 2.450 nonbonded pdb=" H ASN A 426 " pdb=" OD1 ASN A 450 " model vdw 1.553 2.450 nonbonded pdb=" H GLY C 4 " pdb=" OD2 ASP C 7 " model vdw 1.559 2.450 nonbonded pdb=" H ASP C 24 " pdb=" O GLY D 21 " model vdw 1.564 2.450 ... (remaining 393945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 328 through 678 or (resid 679 through 680 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 681 throu \ gh 838 or (resid 839 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or na \ me HD21)) or resid 840 through 1047 or resid 1119 through 1305 or resid 2201 thr \ ough 2209)) selection = (chain 'B' and (resid 328 through 518 or (resid 519 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 520 through 991 or re \ sid 1031 through 1047 or resid 1119 through 1175 or (resid 1176 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 1177 thro \ ugh 1183 or (resid 1184 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 1185 through 1216 or resid 1221 through 1305 or r \ esid 2202 through 2210)) } ncs_group { reference = (chain 'C' and resid 2 through 24) selection = (chain 'E' and (resid 2 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name H )) or resid 9 through 14 or (resid 15 and (name N or name CA \ or name C or name O or name H )) or resid 16 through 24)) selection = (chain 'G' and (resid 2 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name H )) or resid 9 through 14 or (resid 15 and (name N or name CA \ or name C or name O or name H )) or resid 16 through 24)) } ncs_group { reference = (chain 'D' and resid 2 through 24) selection = (chain 'F' and (resid 2 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name H )) or resid 17 through 24)) selection = (chain 'H' and (resid 2 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name H )) or resid 17 through 24)) } 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 group one per residue 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.230 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.660 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15200 Z= 0.208 Angle : 0.660 5.662 20605 Z= 0.374 Chirality : 0.046 0.415 2319 Planarity : 0.004 0.064 2635 Dihedral : 13.660 89.311 5970 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.74 % Favored : 90.87 % Rotamer: Outliers : 0.30 % Allowed : 10.44 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.20), residues: 1819 helix: -1.22 (0.35), residues: 184 sheet: -1.06 (0.24), residues: 436 loop : -1.06 (0.19), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 15 TYR 0.011 0.001 TYR A 737 PHE 0.015 0.001 PHE B 603 TRP 0.006 0.001 TRP B 461 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00425 (15137) covalent geometry : angle 0.65069 (20460) SS BOND : bond 0.00205 ( 44) SS BOND : angle 0.62816 ( 88) hydrogen bonds : bond 0.22312 ( 353) hydrogen bonds : angle 9.60099 ( 927) link_NAG-ASN : bond 0.00248 ( 19) link_NAG-ASN : angle 2.23395 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1184 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 989 MET cc_start: 0.3185 (mtm) cc_final: 0.2889 (mtp) outliers start: 5 outliers final: 5 residues processed: 101 average time/residue: 0.2751 time to fit residues: 41.4779 Evaluate side-chains 99 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 946 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.087319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.059677 restraints weight = 119603.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063341 restraints weight = 52422.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065751 restraints weight = 32467.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.067270 restraints weight = 24318.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.068206 restraints weight = 20294.252| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15200 Z= 0.141 Angle : 0.580 5.657 20605 Z= 0.309 Chirality : 0.047 0.362 2319 Planarity : 0.004 0.054 2635 Dihedral : 6.914 59.678 2407 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.47 % Favored : 91.20 % Rotamer: Outliers : 0.97 % Allowed : 10.02 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.20), residues: 1819 helix: -1.00 (0.36), residues: 201 sheet: -0.98 (0.25), residues: 400 loop : -1.15 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1225 TYR 0.014 0.001 TYR A 737 PHE 0.017 0.001 PHE B1165 TRP 0.004 0.001 TRP B1228 HIS 0.004 0.001 HIS A1216 Details of bonding type rmsd covalent geometry : bond 0.00309 (15137) covalent geometry : angle 0.57153 (20460) SS BOND : bond 0.00207 ( 44) SS BOND : angle 0.55642 ( 88) hydrogen bonds : bond 0.04877 ( 353) hydrogen bonds : angle 7.19017 ( 927) link_NAG-ASN : bond 0.00160 ( 19) link_NAG-ASN : angle 2.00131 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1184 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 GLN cc_start: 0.9008 (mt0) cc_final: 0.8697 (mt0) REVERT: A 961 ARG cc_start: 0.7715 (ptp-170) cc_final: 0.7438 (ptp90) REVERT: B 674 THR cc_start: 0.9213 (m) cc_final: 0.8824 (p) REVERT: B 1036 GLU cc_start: 0.8729 (tp30) cc_final: 0.8527 (tp30) outliers start: 16 outliers final: 11 residues processed: 110 average time/residue: 0.2722 time to fit residues: 45.5210 Evaluate side-chains 105 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 1167 VAL Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A1286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.087216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058735 restraints weight = 118858.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.062375 restraints weight = 53477.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.064753 restraints weight = 33602.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.066275 restraints weight = 25382.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067201 restraints weight = 21303.761| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15200 Z= 0.165 Angle : 0.557 5.123 20605 Z= 0.293 Chirality : 0.045 0.329 2319 Planarity : 0.004 0.057 2635 Dihedral : 6.454 59.447 2403 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.47 % Favored : 91.20 % Rotamer: Outliers : 0.91 % Allowed : 10.86 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.19), residues: 1819 helix: -0.99 (0.36), residues: 201 sheet: -1.08 (0.24), residues: 412 loop : -1.26 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 679 TYR 0.012 0.001 TYR A 737 PHE 0.016 0.001 PHE B1165 TRP 0.015 0.001 TRP A 522 HIS 0.004 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00363 (15137) covalent geometry : angle 0.54719 (20460) SS BOND : bond 0.00290 ( 44) SS BOND : angle 0.62651 ( 88) hydrogen bonds : bond 0.04514 ( 353) hydrogen bonds : angle 6.80027 ( 927) link_NAG-ASN : bond 0.00176 ( 19) link_NAG-ASN : angle 2.01407 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1184 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.7134 (mtp) cc_final: 0.6663 (ttt) REVERT: B 607 SER cc_start: 0.8692 (m) cc_final: 0.8470 (p) REVERT: B 752 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8215 (tt0) outliers start: 15 outliers final: 13 residues processed: 108 average time/residue: 0.2505 time to fit residues: 41.7287 Evaluate side-chains 105 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 1119 ASP Chi-restraints excluded: chain B residue 1167 VAL Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 38 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.086842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.059436 restraints weight = 118252.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.063037 restraints weight = 52606.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065411 restraints weight = 32728.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.066904 restraints weight = 24518.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067749 restraints weight = 20501.183| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15200 Z= 0.137 Angle : 0.535 5.189 20605 Z= 0.280 Chirality : 0.045 0.321 2319 Planarity : 0.003 0.055 2635 Dihedral : 6.095 58.851 2403 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.58 % Favored : 91.15 % Rotamer: Outliers : 0.84 % Allowed : 11.29 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.20), residues: 1819 helix: -0.88 (0.35), residues: 207 sheet: -1.14 (0.24), residues: 414 loop : -1.23 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 961 TYR 0.011 0.001 TYR A1124 PHE 0.016 0.001 PHE B1165 TRP 0.007 0.001 TRP A 522 HIS 0.004 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00307 (15137) covalent geometry : angle 0.52623 (20460) SS BOND : bond 0.00227 ( 44) SS BOND : angle 0.61878 ( 88) hydrogen bonds : bond 0.03679 ( 353) hydrogen bonds : angle 6.45254 ( 927) link_NAG-ASN : bond 0.00156 ( 19) link_NAG-ASN : angle 1.83381 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1184 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 961 ARG cc_start: 0.7727 (ptp-170) cc_final: 0.7487 (ptp90) REVERT: B 607 SER cc_start: 0.8693 (m) cc_final: 0.8473 (p) REVERT: B 752 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8285 (tt0) outliers start: 14 outliers final: 13 residues processed: 103 average time/residue: 0.2535 time to fit residues: 39.7486 Evaluate side-chains 104 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 1119 ASP Chi-restraints excluded: chain B residue 1167 VAL Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 34 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.087055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.059259 restraints weight = 119750.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.062944 restraints weight = 52730.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065361 restraints weight = 32726.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.066876 restraints weight = 24522.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067817 restraints weight = 20494.122| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15200 Z= 0.132 Angle : 0.524 5.257 20605 Z= 0.275 Chirality : 0.045 0.314 2319 Planarity : 0.003 0.053 2635 Dihedral : 5.957 58.074 2403 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.25 % Favored : 91.53 % Rotamer: Outliers : 1.09 % Allowed : 11.23 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.19), residues: 1819 helix: -0.81 (0.36), residues: 201 sheet: -1.14 (0.24), residues: 413 loop : -1.27 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 11 TYR 0.011 0.001 TYR A 737 PHE 0.016 0.001 PHE B1165 TRP 0.006 0.001 TRP A 522 HIS 0.004 0.001 HIS B1216 Details of bonding type rmsd covalent geometry : bond 0.00297 (15137) covalent geometry : angle 0.51678 (20460) SS BOND : bond 0.00197 ( 44) SS BOND : angle 0.55335 ( 88) hydrogen bonds : bond 0.03569 ( 353) hydrogen bonds : angle 6.30048 ( 927) link_NAG-ASN : bond 0.00153 ( 19) link_NAG-ASN : angle 1.76037 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1184 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 961 ARG cc_start: 0.7756 (ptp-170) cc_final: 0.7488 (ptp90) REVERT: B 607 SER cc_start: 0.8726 (m) cc_final: 0.8492 (p) REVERT: B 752 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: B 989 MET cc_start: 0.3163 (mtm) cc_final: 0.2876 (mtp) outliers start: 18 outliers final: 14 residues processed: 106 average time/residue: 0.2689 time to fit residues: 43.0222 Evaluate side-chains 106 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 1119 ASP Chi-restraints excluded: chain B residue 1167 VAL Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 86 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.085637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.057795 restraints weight = 119774.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.061377 restraints weight = 53519.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063732 restraints weight = 33485.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065202 restraints weight = 25175.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.066143 restraints weight = 21138.891| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15200 Z= 0.221 Angle : 0.567 5.349 20605 Z= 0.297 Chirality : 0.046 0.353 2319 Planarity : 0.004 0.058 2635 Dihedral : 6.145 59.710 2403 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.79 % Favored : 90.05 % Rotamer: Outliers : 1.15 % Allowed : 11.35 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -2.10 (0.19), residues: 1819 helix: -1.15 (0.34), residues: 209 sheet: -1.44 (0.24), residues: 422 loop : -1.45 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 679 TYR 0.016 0.001 TYR A 737 PHE 0.017 0.001 PHE B1165 TRP 0.009 0.001 TRP A 748 HIS 0.006 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00485 (15137) covalent geometry : angle 0.55844 (20460) SS BOND : bond 0.00262 ( 44) SS BOND : angle 0.64395 ( 88) hydrogen bonds : bond 0.03690 ( 353) hydrogen bonds : angle 6.36649 ( 927) link_NAG-ASN : bond 0.00199 ( 19) link_NAG-ASN : angle 1.93888 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1184 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 607 SER cc_start: 0.8771 (m) cc_final: 0.8525 (p) REVERT: B 752 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8327 (tt0) outliers start: 19 outliers final: 17 residues processed: 104 average time/residue: 0.2399 time to fit residues: 38.5622 Evaluate side-chains 106 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 726 ASP Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 1119 ASP Chi-restraints excluded: chain B residue 1167 VAL Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 45 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.086623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.058895 restraints weight = 119364.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.062571 restraints weight = 52803.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064953 restraints weight = 32785.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066480 restraints weight = 24612.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.067422 restraints weight = 20562.372| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15200 Z= 0.126 Angle : 0.524 5.311 20605 Z= 0.273 Chirality : 0.045 0.329 2319 Planarity : 0.003 0.053 2635 Dihedral : 5.947 58.811 2403 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.03 % Favored : 91.75 % Rotamer: Outliers : 1.09 % Allowed : 11.35 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.19), residues: 1819 helix: -0.95 (0.35), residues: 209 sheet: -1.35 (0.24), residues: 420 loop : -1.34 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 961 TYR 0.011 0.001 TYR A 737 PHE 0.016 0.001 PHE B1165 TRP 0.004 0.001 TRP A 522 HIS 0.004 0.001 HIS B1216 Details of bonding type rmsd covalent geometry : bond 0.00284 (15137) covalent geometry : angle 0.51669 (20460) SS BOND : bond 0.00193 ( 44) SS BOND : angle 0.55105 ( 88) hydrogen bonds : bond 0.03406 ( 353) hydrogen bonds : angle 6.14056 ( 927) link_NAG-ASN : bond 0.00184 ( 19) link_NAG-ASN : angle 1.74636 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1184 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 970 ASN cc_start: 0.8783 (m-40) cc_final: 0.8436 (p0) REVERT: B 607 SER cc_start: 0.8752 (m) cc_final: 0.8502 (p) REVERT: B 752 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8216 (tt0) outliers start: 18 outliers final: 16 residues processed: 103 average time/residue: 0.2500 time to fit residues: 39.6173 Evaluate side-chains 107 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 1119 ASP Chi-restraints excluded: chain B residue 1167 VAL Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.085374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.057473 restraints weight = 119496.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.061020 restraints weight = 53278.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.063353 restraints weight = 33224.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.064833 restraints weight = 24900.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065767 restraints weight = 20907.428| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15200 Z= 0.251 Angle : 0.584 8.074 20605 Z= 0.305 Chirality : 0.046 0.364 2319 Planarity : 0.004 0.054 2635 Dihedral : 6.170 59.020 2403 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.45 % Favored : 89.33 % Rotamer: Outliers : 1.15 % Allowed : 11.71 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -2.20 (0.19), residues: 1819 helix: -1.18 (0.34), residues: 209 sheet: -1.52 (0.24), residues: 422 loop : -1.53 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 961 TYR 0.017 0.001 TYR A 737 PHE 0.016 0.002 PHE B1165 TRP 0.007 0.001 TRP A 748 HIS 0.006 0.001 HIS A 706 Details of bonding type rmsd covalent geometry : bond 0.00548 (15137) covalent geometry : angle 0.57513 (20460) SS BOND : bond 0.00284 ( 44) SS BOND : angle 0.64788 ( 88) hydrogen bonds : bond 0.03685 ( 353) hydrogen bonds : angle 6.31102 ( 927) link_NAG-ASN : bond 0.00237 ( 19) link_NAG-ASN : angle 1.95283 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1184 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 970 ASN cc_start: 0.8779 (m-40) cc_final: 0.8457 (p0) REVERT: B 607 SER cc_start: 0.8805 (m) cc_final: 0.8540 (p) REVERT: B 752 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: B 989 MET cc_start: 0.3108 (mtm) cc_final: 0.2810 (mtp) outliers start: 19 outliers final: 17 residues processed: 102 average time/residue: 0.2544 time to fit residues: 40.4501 Evaluate side-chains 106 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 1119 ASP Chi-restraints excluded: chain B residue 1167 VAL Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 56 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.087604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.059844 restraints weight = 118599.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063432 restraints weight = 54415.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065809 restraints weight = 34392.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067294 restraints weight = 25936.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068212 restraints weight = 21805.714| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15200 Z= 0.125 Angle : 0.528 6.769 20605 Z= 0.274 Chirality : 0.045 0.333 2319 Planarity : 0.003 0.051 2635 Dihedral : 5.929 59.029 2403 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.86 % Favored : 91.92 % Rotamer: Outliers : 0.97 % Allowed : 11.83 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.19), residues: 1819 helix: -0.98 (0.34), residues: 209 sheet: -1.37 (0.24), residues: 420 loop : -1.36 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.012 0.001 TYR A 737 PHE 0.016 0.001 PHE B1165 TRP 0.009 0.001 TRP A 748 HIS 0.004 0.001 HIS B1216 Details of bonding type rmsd covalent geometry : bond 0.00284 (15137) covalent geometry : angle 0.52116 (20460) SS BOND : bond 0.00189 ( 44) SS BOND : angle 0.54148 ( 88) hydrogen bonds : bond 0.03303 ( 353) hydrogen bonds : angle 6.06902 ( 927) link_NAG-ASN : bond 0.00191 ( 19) link_NAG-ASN : angle 1.71940 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1184 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 970 ASN cc_start: 0.8696 (m-40) cc_final: 0.8446 (p0) REVERT: B 752 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8320 (tt0) outliers start: 16 outliers final: 13 residues processed: 101 average time/residue: 0.2565 time to fit residues: 40.3594 Evaluate side-chains 99 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 1167 VAL Chi-restraints excluded: chain G residue 7 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 144 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 111 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.087804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.060166 restraints weight = 118547.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063740 restraints weight = 54211.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066119 restraints weight = 34235.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.067596 restraints weight = 25811.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.068365 restraints weight = 21694.026| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15200 Z= 0.122 Angle : 0.518 6.207 20605 Z= 0.269 Chirality : 0.045 0.317 2319 Planarity : 0.003 0.042 2635 Dihedral : 5.734 56.958 2403 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.58 % Favored : 91.20 % Rotamer: Outliers : 0.84 % Allowed : 12.01 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.19), residues: 1819 helix: -0.91 (0.35), residues: 209 sheet: -1.32 (0.24), residues: 420 loop : -1.34 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.010 0.001 TYR A 737 PHE 0.015 0.001 PHE B1165 TRP 0.013 0.001 TRP A 748 HIS 0.004 0.001 HIS B1216 Details of bonding type rmsd covalent geometry : bond 0.00275 (15137) covalent geometry : angle 0.51117 (20460) SS BOND : bond 0.00176 ( 44) SS BOND : angle 0.50308 ( 88) hydrogen bonds : bond 0.03188 ( 353) hydrogen bonds : angle 5.95762 ( 927) link_NAG-ASN : bond 0.00178 ( 19) link_NAG-ASN : angle 1.63853 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1184 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 970 ASN cc_start: 0.8670 (m-40) cc_final: 0.8422 (p0) REVERT: B 752 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8356 (tt0) outliers start: 14 outliers final: 13 residues processed: 99 average time/residue: 0.2576 time to fit residues: 39.4013 Evaluate side-chains 99 residues out of total 1667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 1167 VAL Chi-restraints excluded: chain G residue 7 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 1 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.087555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.059789 restraints weight = 119189.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.063404 restraints weight = 54626.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065782 restraints weight = 34449.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067242 restraints weight = 26003.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.068177 restraints weight = 21890.414| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15200 Z= 0.131 Angle : 0.522 6.170 20605 Z= 0.270 Chirality : 0.045 0.313 2319 Planarity : 0.003 0.043 2635 Dihedral : 5.712 56.800 2403 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.36 % Favored : 91.42 % Rotamer: Outliers : 0.78 % Allowed : 12.43 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.19), residues: 1819 helix: -0.91 (0.35), residues: 209 sheet: -1.33 (0.24), residues: 419 loop : -1.37 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.011 0.001 TYR A 737 PHE 0.015 0.001 PHE B1165 TRP 0.017 0.001 TRP A 748 HIS 0.004 0.001 HIS B1216 Details of bonding type rmsd covalent geometry : bond 0.00294 (15137) covalent geometry : angle 0.51555 (20460) SS BOND : bond 0.00187 ( 44) SS BOND : angle 0.51519 ( 88) hydrogen bonds : bond 0.03214 ( 353) hydrogen bonds : angle 5.91178 ( 927) link_NAG-ASN : bond 0.00173 ( 19) link_NAG-ASN : angle 1.63222 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4350.22 seconds wall clock time: 75 minutes 18.89 seconds (4518.89 seconds total)