Starting phenix.real_space_refine on Thu Mar 5 21:34:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzm_48761/03_2026/9mzm_48761.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzm_48761/03_2026/9mzm_48761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mzm_48761/03_2026/9mzm_48761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzm_48761/03_2026/9mzm_48761.map" model { file = "/net/cci-nas-00/data/ceres_data/9mzm_48761/03_2026/9mzm_48761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzm_48761/03_2026/9mzm_48761.cif" } resolution = 3.86 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= 0.003 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 139 5.16 5 C 15933 2.51 5 N 4088 2.21 5 O 4705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24865 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 6085 Classifications: {'peptide': 769} Link IDs: {'PTRANS': 28, 'TRANS': 740} Chain breaks: 1 Chain: "B" Number of atoms: 6108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6108 Classifications: {'peptide': 772} Link IDs: {'PTRANS': 29, 'TRANS': 742} Chain breaks: 1 Chain: "C" Number of atoms: 6109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6109 Classifications: {'peptide': 772} Link IDs: {'PTRANS': 29, 'TRANS': 742} Chain breaks: 1 Chain: "D" Number of atoms: 6103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6103 Classifications: {'peptide': 771} Link IDs: {'PTRANS': 29, 'TRANS': 741} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.14, per 1000 atoms: 0.25 Number of scatterers: 24865 At special positions: 0 Unit cell: (156.88, 100.7, 187.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 139 16.00 O 4705 8.00 N 4088 7.00 C 15933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.04 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS B 802 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 676 " - pdb=" SG CYS D 802 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A1001 " - " ASN A 412 " " NAG A1002 " - " ASN A 546 " " NAG A1003 " - " ASN A 749 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 751 " " NAG C1001 " - " ASN C 412 " " NAG C1002 " - " ASN C 751 " " NAG C1003 " - " ASN C 430 " " NAG D1001 " - " ASN D 751 " " NAG D1002 " - " ASN D 275 " " NAG D1003 " - " ASN D 412 " " NAG D1004 " - " ASN D 546 " " NAG E 1 " - " ASN A 275 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN B 546 " " NAG H 1 " - " ASN B 67 " " NAG I 1 " - " ASN C 378 " " NAG J 1 " - " ASN C 275 " " NAG K 1 " - " ASN C 67 " " NAG L 1 " - " ASN D 67 " " NAG M 1 " - " ASN D 378 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 972.7 milliseconds 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5752 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 37 sheets defined 45.4% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.921A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 4.067A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.550A pdb=" N LYS A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.980A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.505A pdb=" N MET A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.944A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.506A pdb=" N PHE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.533A pdb=" N PHE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 4.238A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.686A pdb=" N PHE A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 665 Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.621A pdb=" N LEU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.505A pdb=" N THR A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.934A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.578A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 788 removed outlier: 3.990A pdb=" N ASP A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 793 removed outlier: 3.637A pdb=" N HIS A 792 " --> pdb=" O GLY A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 846 removed outlier: 6.241A pdb=" N GLY A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.546A pdb=" N ALA B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.758A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 4.296A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.658A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 266 through 271 removed outlier: 4.625A pdb=" N TYR B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 317 through 337 removed outlier: 3.528A pdb=" N ALA B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 560 through 584 Processing helix chain 'B' and resid 630 through 661 removed outlier: 3.649A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 Processing helix chain 'B' and resid 688 through 697 removed outlier: 3.719A pdb=" N THR B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.547A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.589A pdb=" N THR B 746 " --> pdb=" O ILE B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 785 removed outlier: 4.312A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 798 Processing helix chain 'B' and resid 822 through 844 Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.548A pdb=" N ILE C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.814A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 removed outlier: 4.220A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.535A pdb=" N MET C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 298 removed outlier: 3.629A pdb=" N SER C 290 " --> pdb=" O ASN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 337 Processing helix chain 'C' and resid 356 through 365 Processing helix chain 'C' and resid 461 through 475 Processing helix chain 'C' and resid 502 through 507 Processing helix chain 'C' and resid 520 through 526 removed outlier: 3.974A pdb=" N VAL C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 584 Processing helix chain 'C' and resid 630 through 665 Processing helix chain 'C' and resid 670 through 677 removed outlier: 4.235A pdb=" N LEU C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 696 Processing helix chain 'C' and resid 699 through 712 removed outlier: 4.033A pdb=" N ARG C 712 " --> pdb=" O PHE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 731 removed outlier: 4.014A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 749 removed outlier: 3.571A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 789 removed outlier: 3.817A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 796 removed outlier: 3.906A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU C 796 " --> pdb=" O HIS C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 842 removed outlier: 3.889A pdb=" N PHE C 824 " --> pdb=" O ILE C 820 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 101 Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.919A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 4.382A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 4.455A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 266 through 271 removed outlier: 4.591A pdb=" N TYR D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 300 Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.540A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.716A pdb=" N GLU D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 432 removed outlier: 3.547A pdb=" N SER D 432 " --> pdb=" O SER D 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 429 through 432' Processing helix chain 'D' and resid 454 through 457 removed outlier: 4.081A pdb=" N ASP D 457 " --> pdb=" O TYR D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 454 through 457' Processing helix chain 'D' and resid 462 through 474 Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.808A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.677A pdb=" N LEU D 556 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 584 Processing helix chain 'D' and resid 632 through 661 removed outlier: 3.875A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 676 Processing helix chain 'D' and resid 688 through 697 removed outlier: 4.331A pdb=" N THR D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.680A pdb=" N ARG D 712 " --> pdb=" O PHE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 717 Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 776 through 788 removed outlier: 3.722A pdb=" N GLU D 788 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 796 Processing helix chain 'D' and resid 816 through 844 removed outlier: 6.317A pdb=" N GLY D 822 " --> pdb=" O GLN D 818 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE D 824 " --> pdb=" O ILE D 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 83 removed outlier: 5.961A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA A 104 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ARG A 37 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 106 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 39 " --> pdb=" O ILE A 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199 removed outlier: 7.924A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 199 removed outlier: 4.638A pdb=" N HIS A 225 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 227 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 254 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 279 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 390 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 406 removed outlier: 4.065A pdb=" N ASP A 406 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 437 removed outlier: 3.599A pdb=" N VAL A 435 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A 437 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA8, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA9, first strand: chain 'A' and resid 682 through 684 removed outlier: 3.609A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 542 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 753 " --> pdb=" O TYR A 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 682 through 684 Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 82 removed outlier: 6.639A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA B 105 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.149A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.694A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 432 through 435 removed outlier: 3.558A pdb=" N GLU B 479 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB7, first strand: chain 'B' and resid 682 through 683 removed outlier: 6.053A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 682 through 683 removed outlier: 6.053A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 74 through 83 removed outlier: 6.324A pdb=" N HIS C 34 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR C 77 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AC2, first strand: chain 'C' and resid 198 through 203 removed outlier: 6.505A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS C 225 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE C 256 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 433 through 437 removed outlier: 3.792A pdb=" N THR C 437 " --> pdb=" O ARG C 481 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC5, first strand: chain 'C' and resid 490 through 491 removed outlier: 3.752A pdb=" N ALA C 490 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AC7, first strand: chain 'C' and resid 534 through 535 removed outlier: 3.967A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 540 through 543 removed outlier: 3.897A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 753 " --> pdb=" O TYR C 542 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.907A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 35 through 37 removed outlier: 6.016A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 80 through 83 removed outlier: 7.128A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE D 41 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.075A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 369 through 370 Processing sheet with id=AD5, first strand: chain 'D' and resid 389 through 395 removed outlier: 3.578A pdb=" N GLY D 403 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER D 393 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS D 401 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS D 395 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 434 through 436 Processing sheet with id=AD7, first strand: chain 'D' and resid 444 through 446 removed outlier: 3.620A pdb=" N LEU D 445 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AD9, first strand: chain 'D' and resid 535 through 536 Processing sheet with id=AE1, first strand: chain 'D' and resid 682 through 683 removed outlier: 6.276A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 3018 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: 5.05 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7825 1.34 - 1.46: 5969 1.46 - 1.58: 11368 1.58 - 1.70: 0 1.70 - 1.82: 238 Bond restraints: 25400 Sorted by residual: bond pdb=" N THR D 660 " pdb=" CA THR D 660 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.27e-02 6.20e+03 7.15e+00 bond pdb=" N MET A 664 " pdb=" CA MET A 664 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.33e-02 5.65e+03 5.21e+00 bond pdb=" N MET C 664 " pdb=" CA MET C 664 " ideal model delta sigma weight residual 1.457 1.485 -0.029 1.33e-02 5.65e+03 4.65e+00 bond pdb=" CB GLN D 714 " pdb=" CG GLN D 714 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.72e+00 bond pdb=" CB ASP D 313 " pdb=" CG ASP D 313 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.65e+00 ... (remaining 25395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 33909 2.14 - 4.28: 384 4.28 - 6.42: 62 6.42 - 8.57: 18 8.57 - 10.71: 8 Bond angle restraints: 34381 Sorted by residual: angle pdb=" CA LYS B 790 " pdb=" CB LYS B 790 " pdb=" CG LYS B 790 " ideal model delta sigma weight residual 114.10 122.45 -8.35 2.00e+00 2.50e-01 1.74e+01 angle pdb=" CA ARG C 68 " pdb=" CB ARG C 68 " pdb=" CG ARG C 68 " ideal model delta sigma weight residual 114.10 122.11 -8.01 2.00e+00 2.50e-01 1.60e+01 angle pdb=" CB MET B 664 " pdb=" CG MET B 664 " pdb=" SD MET B 664 " ideal model delta sigma weight residual 112.70 123.19 -10.49 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CB MET D 248 " pdb=" CG MET D 248 " pdb=" SD MET D 248 " ideal model delta sigma weight residual 112.70 122.64 -9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C2 NAG F 1 " pdb=" N2 NAG F 1 " pdb=" C7 NAG F 1 " ideal model delta sigma weight residual 124.56 134.16 -9.60 3.00e+00 1.11e-01 1.02e+01 ... (remaining 34376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13471 17.98 - 35.97: 1635 35.97 - 53.95: 382 53.95 - 71.93: 58 71.93 - 89.92: 21 Dihedral angle restraints: 15567 sinusoidal: 6623 harmonic: 8944 Sorted by residual: dihedral pdb=" CB CYS C 676 " pdb=" SG CYS C 676 " pdb=" SG CYS D 802 " pdb=" CB CYS D 802 " ideal model delta sinusoidal sigma weight residual 93.00 11.11 81.89 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS A 750 " pdb=" SG CYS A 750 " pdb=" SG CYS A 804 " pdb=" CB CYS A 804 " ideal model delta sinusoidal sigma weight residual -86.00 -134.96 48.96 1 1.00e+01 1.00e-02 3.30e+01 dihedral pdb=" CB CYS D 750 " pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " pdb=" CB CYS D 804 " ideal model delta sinusoidal sigma weight residual -86.00 -38.77 -47.23 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 15564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3188 0.050 - 0.099: 644 0.099 - 0.149: 105 0.149 - 0.198: 8 0.198 - 0.248: 2 Chirality restraints: 3947 Sorted by residual: chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.24 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 546 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.02e+00 ... (remaining 3944 not shown) Planarity restraints: 4330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 169 " 0.023 2.00e-02 2.50e+03 2.55e-02 1.63e+01 pdb=" CG TRP A 169 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP A 169 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP A 169 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 169 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 169 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 169 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 169 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 169 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 169 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 798 " -0.021 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP B 798 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 798 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 798 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 798 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 798 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 798 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 798 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 798 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 798 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 34 " 0.019 2.00e-02 2.50e+03 2.20e-02 7.26e+00 pdb=" CG HIS B 34 " -0.047 2.00e-02 2.50e+03 pdb=" ND1 HIS B 34 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 34 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS B 34 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 34 " 0.003 2.00e-02 2.50e+03 ... (remaining 4327 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 12329 2.97 - 3.45: 26263 3.45 - 3.93: 40124 3.93 - 4.42: 45431 4.42 - 4.90: 72528 Nonbonded interactions: 196675 Sorted by model distance: nonbonded pdb=" O ARG C 68 " pdb=" NE ARG C 68 " model vdw 2.487 3.120 nonbonded pdb=" N ASP C 672 " pdb=" OD1 ASP C 672 " model vdw 2.527 3.120 nonbonded pdb=" N GLN D 714 " pdb=" OE1 GLN D 714 " model vdw 2.529 3.120 nonbonded pdb=" O LEU C 556 " pdb=" O LEU C 559 " model vdw 2.571 3.040 nonbonded pdb=" O MET B 248 " pdb=" OG SER B 272 " model vdw 2.577 3.040 ... (remaining 196670 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 33 through 844 or resid 1002 through 1004)) selection = (chain 'B' and (resid 33 through 584 or resid 630 through 1003)) selection = (chain 'C' and (resid 33 through 584 or resid 630 through 844 or resid 1002 thro \ ugh 1004)) selection = (chain 'D' and (resid 33 through 584 or resid 630 through 844 or resid 1003 thro \ ugh 1005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.130 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.003 0.039 25440 Z= 0.133 Angle : 0.612 10.707 34491 Z= 0.300 Chirality : 0.041 0.248 3947 Planarity : 0.003 0.051 4309 Dihedral : 15.952 89.915 9785 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.91 % Allowed : 19.47 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.15), residues: 3068 helix: 0.15 (0.14), residues: 1315 sheet: -2.24 (0.30), residues: 317 loop : -1.41 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 184 TYR 0.026 0.001 TYR B 443 PHE 0.013 0.001 PHE A 337 TRP 0.063 0.002 TRP A 169 HIS 0.026 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00297 (25400) covalent geometry : angle 0.59964 (34381) SS BOND : bond 0.00331 ( 10) SS BOND : angle 1.26619 ( 20) hydrogen bonds : bond 0.20820 ( 1029) hydrogen bonds : angle 7.38333 ( 3018) link_BETA1-4 : bond 0.00501 ( 9) link_BETA1-4 : angle 2.11227 ( 27) link_NAG-ASN : bond 0.00317 ( 21) link_NAG-ASN : angle 2.52744 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 281 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7834 (tm-30) REVERT: A 504 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7746 (tm-30) REVERT: A 658 PHE cc_start: 0.8085 (t80) cc_final: 0.7825 (t80) REVERT: A 737 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7502 (ppp) REVERT: B 78 TYR cc_start: 0.7881 (p90) cc_final: 0.7647 (p90) REVERT: B 340 MET cc_start: 0.7848 (tmm) cc_final: 0.7421 (ppp) REVERT: B 360 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7970 (mmm) REVERT: B 696 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7313 (tptt) REVERT: C 743 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6956 (tt0) REVERT: D 50 MET cc_start: 0.7057 (tmm) cc_final: 0.6624 (tmm) REVERT: D 257 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.9103 (t) REVERT: D 360 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7563 (ttm) REVERT: D 439 LEU cc_start: 0.8040 (mt) cc_final: 0.7279 (pp) REVERT: D 645 LEU cc_start: 0.8419 (mm) cc_final: 0.8118 (mm) outliers start: 51 outliers final: 38 residues processed: 312 average time/residue: 0.1570 time to fit residues: 81.2935 Evaluate side-chains 311 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 268 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.181071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.157828 restraints weight = 39849.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.149485 restraints weight = 48470.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.147681 restraints weight = 45380.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.148495 restraints weight = 41913.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.148762 restraints weight = 28526.030| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25440 Z= 0.166 Angle : 0.596 9.646 34491 Z= 0.297 Chirality : 0.042 0.233 3947 Planarity : 0.004 0.051 4309 Dihedral : 6.811 62.492 4046 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.14 % Allowed : 19.99 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.15), residues: 3068 helix: 0.84 (0.14), residues: 1317 sheet: -2.20 (0.28), residues: 358 loop : -1.39 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 184 TYR 0.017 0.001 TYR B 443 PHE 0.012 0.001 PHE A 337 TRP 0.025 0.001 TRP A 169 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00383 (25400) covalent geometry : angle 0.58354 (34381) SS BOND : bond 0.00387 ( 10) SS BOND : angle 1.33099 ( 20) hydrogen bonds : bond 0.04156 ( 1029) hydrogen bonds : angle 4.73400 ( 3018) link_BETA1-4 : bond 0.00449 ( 9) link_BETA1-4 : angle 2.10471 ( 27) link_NAG-ASN : bond 0.00374 ( 21) link_NAG-ASN : angle 2.46891 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 290 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 737 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8044 (ptt) REVERT: B 225 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7615 (m-70) REVERT: B 269 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: B 353 TRP cc_start: 0.7320 (OUTLIER) cc_final: 0.6635 (t60) REVERT: B 360 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.8033 (mmm) REVERT: B 696 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7402 (tptt) REVERT: B 709 MET cc_start: 0.7248 (ptp) cc_final: 0.7004 (ptp) REVERT: B 811 GLU cc_start: 0.5531 (OUTLIER) cc_final: 0.5209 (tp30) REVERT: C 262 PHE cc_start: 0.7168 (p90) cc_final: 0.6830 (p90) REVERT: C 316 MET cc_start: 0.8162 (mmt) cc_final: 0.7375 (mmt) REVERT: C 431 ARG cc_start: 0.7991 (mpp-170) cc_final: 0.7781 (mpp-170) REVERT: C 743 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6918 (tt0) REVERT: D 298 MET cc_start: 0.7043 (mpp) cc_final: 0.6825 (mpp) REVERT: D 350 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7720 (t-90) REVERT: D 360 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7878 (mmm) REVERT: D 645 LEU cc_start: 0.8272 (mm) cc_final: 0.8050 (mm) outliers start: 84 outliers final: 42 residues processed: 351 average time/residue: 0.1430 time to fit residues: 84.8405 Evaluate side-chains 318 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 673 ASP Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 37 optimal weight: 0.0170 chunk 290 optimal weight: 8.9990 chunk 151 optimal weight: 30.0000 chunk 247 optimal weight: 5.9990 chunk 218 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 216 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 255 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.180957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.155109 restraints weight = 39868.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.145349 restraints weight = 42185.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.145127 restraints weight = 41099.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.146526 restraints weight = 32897.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.146735 restraints weight = 25459.198| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25440 Z= 0.152 Angle : 0.587 10.055 34491 Z= 0.288 Chirality : 0.041 0.248 3947 Planarity : 0.004 0.051 4309 Dihedral : 6.414 59.862 4009 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.14 % Allowed : 20.55 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 3068 helix: 1.05 (0.14), residues: 1315 sheet: -2.16 (0.28), residues: 371 loop : -1.40 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 184 TYR 0.017 0.001 TYR A 462 PHE 0.016 0.001 PHE A 166 TRP 0.021 0.001 TRP B 798 HIS 0.016 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00351 (25400) covalent geometry : angle 0.57424 (34381) SS BOND : bond 0.00274 ( 10) SS BOND : angle 1.97595 ( 20) hydrogen bonds : bond 0.03743 ( 1029) hydrogen bonds : angle 4.47781 ( 3018) link_BETA1-4 : bond 0.00445 ( 9) link_BETA1-4 : angle 2.07712 ( 27) link_NAG-ASN : bond 0.00362 ( 21) link_NAG-ASN : angle 2.41218 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 286 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 709 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8046 (mtp) REVERT: A 735 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7567 (t80) REVERT: B 269 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 353 TRP cc_start: 0.7302 (OUTLIER) cc_final: 0.6572 (t60) REVERT: B 696 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7427 (tptt) REVERT: B 811 GLU cc_start: 0.5628 (OUTLIER) cc_final: 0.5235 (tp30) REVERT: C 316 MET cc_start: 0.8329 (mmt) cc_final: 0.8080 (mmt) REVERT: C 540 ILE cc_start: 0.9070 (mt) cc_final: 0.8867 (mt) REVERT: C 743 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7023 (tt0) REVERT: D 298 MET cc_start: 0.7145 (mpp) cc_final: 0.6866 (mpp) REVERT: D 350 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7723 (t-90) REVERT: D 360 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7812 (mmm) REVERT: D 645 LEU cc_start: 0.8269 (mm) cc_final: 0.8040 (mm) REVERT: D 806 GLU cc_start: 0.3460 (OUTLIER) cc_final: 0.2331 (pt0) outliers start: 84 outliers final: 56 residues processed: 350 average time/residue: 0.1530 time to fit residues: 89.6454 Evaluate side-chains 331 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 266 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 521 TYR Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 673 ASP Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 806 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 94 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 305 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 262 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 150 optimal weight: 0.1980 chunk 274 optimal weight: 20.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 749 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.181371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.155611 restraints weight = 39642.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.146000 restraints weight = 41899.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.144220 restraints weight = 39394.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145398 restraints weight = 33061.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145664 restraints weight = 25276.497| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25440 Z= 0.145 Angle : 0.583 10.153 34491 Z= 0.286 Chirality : 0.042 0.230 3947 Planarity : 0.004 0.051 4309 Dihedral : 6.195 57.446 4001 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.77 % Allowed : 20.81 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 3068 helix: 1.18 (0.15), residues: 1309 sheet: -2.15 (0.27), residues: 381 loop : -1.41 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 184 TYR 0.011 0.001 TYR C 571 PHE 0.036 0.001 PHE A 555 TRP 0.024 0.001 TRP A 169 HIS 0.009 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00336 (25400) covalent geometry : angle 0.57128 (34381) SS BOND : bond 0.00254 ( 10) SS BOND : angle 1.60668 ( 20) hydrogen bonds : bond 0.03430 ( 1029) hydrogen bonds : angle 4.31608 ( 3018) link_BETA1-4 : bond 0.00426 ( 9) link_BETA1-4 : angle 2.04732 ( 27) link_NAG-ASN : bond 0.00361 ( 21) link_NAG-ASN : angle 2.34916 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 281 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 709 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8157 (mtp) REVERT: A 735 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7455 (t80) REVERT: B 225 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7538 (m-70) REVERT: B 262 PHE cc_start: 0.7774 (m-80) cc_final: 0.7328 (m-80) REVERT: B 269 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: B 280 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.6575 (tmm-80) REVERT: B 353 TRP cc_start: 0.7276 (OUTLIER) cc_final: 0.6562 (t60) REVERT: B 696 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7434 (tptt) REVERT: B 811 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.5249 (tp30) REVERT: C 743 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7037 (tt0) REVERT: D 350 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7764 (t-90) REVERT: D 360 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8161 (mmm) REVERT: D 645 LEU cc_start: 0.8337 (mm) cc_final: 0.8086 (mm) REVERT: D 806 GLU cc_start: 0.3325 (OUTLIER) cc_final: 0.2173 (pt0) outliers start: 101 outliers final: 63 residues processed: 365 average time/residue: 0.1519 time to fit residues: 92.9612 Evaluate side-chains 341 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 267 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 673 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 806 GLU Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 116 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 261 optimal weight: 0.4980 chunk 53 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 206 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** 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 = 0.4280 r_free = 0.4280 target = 0.178773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.155418 restraints weight = 39800.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145048 restraints weight = 37152.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.142787 restraints weight = 37333.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.142981 restraints weight = 32279.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.143007 restraints weight = 29143.196| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25440 Z= 0.211 Angle : 0.637 10.273 34491 Z= 0.312 Chirality : 0.043 0.268 3947 Planarity : 0.004 0.051 4309 Dihedral : 6.303 58.615 3998 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.30 % Allowed : 21.45 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 3068 helix: 1.20 (0.15), residues: 1307 sheet: -2.33 (0.26), residues: 390 loop : -1.42 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 184 TYR 0.014 0.001 TYR B 443 PHE 0.025 0.001 PHE A 166 TRP 0.019 0.002 TRP B 798 HIS 0.010 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00493 (25400) covalent geometry : angle 0.62620 (34381) SS BOND : bond 0.00435 ( 10) SS BOND : angle 1.27945 ( 20) hydrogen bonds : bond 0.03555 ( 1029) hydrogen bonds : angle 4.38505 ( 3018) link_BETA1-4 : bond 0.00349 ( 9) link_BETA1-4 : angle 2.08988 ( 27) link_NAG-ASN : bond 0.00440 ( 21) link_NAG-ASN : angle 2.39496 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 274 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8119 (mptt) REVERT: A 504 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 538 ILE cc_start: 0.8890 (mm) cc_final: 0.8577 (mm) REVERT: A 709 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: B 269 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8159 (m-80) REVERT: B 353 TRP cc_start: 0.7291 (OUTLIER) cc_final: 0.6616 (t60) REVERT: B 811 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.5343 (tp30) REVERT: C 743 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: D 50 MET cc_start: 0.7235 (tmm) cc_final: 0.6937 (tmm) REVERT: D 160 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8833 (tt) REVERT: D 257 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9123 (m) REVERT: D 269 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: D 298 MET cc_start: 0.7180 (mpp) cc_final: 0.6904 (mmm) REVERT: D 645 LEU cc_start: 0.8340 (mm) cc_final: 0.8118 (mm) outliers start: 115 outliers final: 81 residues processed: 365 average time/residue: 0.1503 time to fit residues: 92.6084 Evaluate side-chains 351 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 262 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 673 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 746 THR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 283 optimal weight: 6.9990 chunk 150 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 256 optimal weight: 10.0000 chunk 290 optimal weight: 0.0570 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.183444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.154690 restraints weight = 39685.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.154222 restraints weight = 53200.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.152394 restraints weight = 32628.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.151961 restraints weight = 31789.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.152703 restraints weight = 24224.411| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25440 Z= 0.106 Angle : 0.579 12.035 34491 Z= 0.283 Chirality : 0.041 0.271 3947 Planarity : 0.003 0.051 4309 Dihedral : 5.896 58.366 3994 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.06 % Allowed : 22.94 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.16), residues: 3068 helix: 1.30 (0.15), residues: 1306 sheet: -2.23 (0.27), residues: 373 loop : -1.41 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 184 TYR 0.018 0.001 TYR C 86 PHE 0.023 0.001 PHE A 555 TRP 0.014 0.001 TRP B 798 HIS 0.006 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00237 (25400) covalent geometry : angle 0.56872 (34381) SS BOND : bond 0.00212 ( 10) SS BOND : angle 0.99749 ( 20) hydrogen bonds : bond 0.03120 ( 1029) hydrogen bonds : angle 4.13025 ( 3018) link_BETA1-4 : bond 0.00511 ( 9) link_BETA1-4 : angle 1.99609 ( 27) link_NAG-ASN : bond 0.00400 ( 21) link_NAG-ASN : angle 2.27555 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 289 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8099 (mptt) REVERT: A 534 MET cc_start: 0.7026 (mtt) cc_final: 0.6812 (mtt) REVERT: A 538 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8560 (mm) REVERT: A 735 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7478 (t80) REVERT: A 754 GLN cc_start: 0.8584 (pp30) cc_final: 0.8369 (pp30) REVERT: B 269 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: B 280 ARG cc_start: 0.8068 (tmm-80) cc_final: 0.7863 (tmm-80) REVERT: B 340 MET cc_start: 0.7538 (tmm) cc_final: 0.6990 (ppp) REVERT: B 353 TRP cc_start: 0.7243 (OUTLIER) cc_final: 0.6613 (t60) REVERT: B 811 GLU cc_start: 0.5568 (OUTLIER) cc_final: 0.5205 (tp30) REVERT: C 258 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8566 (t) REVERT: C 400 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: C 743 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: D 50 MET cc_start: 0.7118 (tmm) cc_final: 0.6838 (tmm) REVERT: D 298 MET cc_start: 0.7091 (mpp) cc_final: 0.6824 (mmm) REVERT: D 645 LEU cc_start: 0.8283 (mm) cc_final: 0.8064 (mm) outliers start: 82 outliers final: 52 residues processed: 357 average time/residue: 0.1420 time to fit residues: 84.4192 Evaluate side-chains 326 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 673 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 685 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 78 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 266 optimal weight: 0.0470 chunk 135 optimal weight: 20.0000 chunk 201 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 165 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** 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 = 0.4301 r_free = 0.4301 target = 0.180678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.154639 restraints weight = 39611.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.146011 restraints weight = 42883.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.144260 restraints weight = 36025.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145499 restraints weight = 33543.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145590 restraints weight = 24815.529| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25440 Z= 0.152 Angle : 0.600 10.328 34491 Z= 0.292 Chirality : 0.042 0.306 3947 Planarity : 0.004 0.051 4309 Dihedral : 5.899 59.910 3994 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.21 % Allowed : 23.21 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.16), residues: 3068 helix: 1.31 (0.15), residues: 1308 sheet: -2.15 (0.26), residues: 397 loop : -1.42 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 184 TYR 0.017 0.001 TYR A 462 PHE 0.018 0.001 PHE A 555 TRP 0.026 0.001 TRP C 640 HIS 0.007 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00359 (25400) covalent geometry : angle 0.59031 (34381) SS BOND : bond 0.00438 ( 10) SS BOND : angle 0.86594 ( 20) hydrogen bonds : bond 0.03234 ( 1029) hydrogen bonds : angle 4.14952 ( 3018) link_BETA1-4 : bond 0.00408 ( 9) link_BETA1-4 : angle 2.00827 ( 27) link_NAG-ASN : bond 0.00347 ( 21) link_NAG-ASN : angle 2.28567 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 269 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 ASP cc_start: 0.7956 (t0) cc_final: 0.7646 (t0) REVERT: A 504 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 538 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8567 (mm) REVERT: B 225 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7513 (m-70) REVERT: B 269 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: B 353 TRP cc_start: 0.7321 (OUTLIER) cc_final: 0.6609 (t60) REVERT: B 811 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5274 (tp30) REVERT: C 234 MET cc_start: 0.7492 (tpp) cc_final: 0.7253 (tpp) REVERT: C 743 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: D 50 MET cc_start: 0.7180 (tmm) cc_final: 0.6870 (tmm) REVERT: D 257 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9095 (t) REVERT: D 360 MET cc_start: 0.8012 (mmm) cc_final: 0.7576 (tpt) REVERT: D 645 LEU cc_start: 0.8286 (mm) cc_final: 0.8069 (mm) outliers start: 86 outliers final: 61 residues processed: 339 average time/residue: 0.1523 time to fit residues: 86.6075 Evaluate side-chains 328 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 673 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 685 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 143 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 262 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 350 HIS ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.181735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.159003 restraints weight = 39753.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.150057 restraints weight = 41998.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.145757 restraints weight = 50382.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.147490 restraints weight = 43261.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.147501 restraints weight = 30574.306| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25440 Z= 0.129 Angle : 0.598 11.565 34491 Z= 0.289 Chirality : 0.042 0.293 3947 Planarity : 0.003 0.050 4309 Dihedral : 5.853 59.225 3994 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.99 % Allowed : 23.36 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 3068 helix: 1.33 (0.15), residues: 1308 sheet: -2.13 (0.26), residues: 403 loop : -1.41 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 184 TYR 0.034 0.001 TYR A 462 PHE 0.018 0.001 PHE A 555 TRP 0.020 0.001 TRP C 640 HIS 0.006 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00301 (25400) covalent geometry : angle 0.58795 (34381) SS BOND : bond 0.00150 ( 10) SS BOND : angle 0.81601 ( 20) hydrogen bonds : bond 0.03144 ( 1029) hydrogen bonds : angle 4.09618 ( 3018) link_BETA1-4 : bond 0.00440 ( 9) link_BETA1-4 : angle 1.98740 ( 27) link_NAG-ASN : bond 0.00342 ( 21) link_NAG-ASN : angle 2.25046 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 273 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 ASP cc_start: 0.7946 (t0) cc_final: 0.7566 (t0) REVERT: A 538 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8559 (mm) REVERT: A 540 ILE cc_start: 0.9013 (mt) cc_final: 0.8678 (mt) REVERT: A 735 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7594 (t80) REVERT: B 269 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: B 340 MET cc_start: 0.7588 (tmm) cc_final: 0.7049 (ppp) REVERT: B 353 TRP cc_start: 0.7293 (OUTLIER) cc_final: 0.6654 (t60) REVERT: B 811 GLU cc_start: 0.5884 (OUTLIER) cc_final: 0.5300 (tp30) REVERT: C 400 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: C 743 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: C 768 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8010 (m) REVERT: D 50 MET cc_start: 0.7183 (tmm) cc_final: 0.6861 (tmm) REVERT: D 257 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9024 (t) REVERT: D 360 MET cc_start: 0.8087 (mmm) cc_final: 0.7706 (tpt) REVERT: D 645 LEU cc_start: 0.8254 (mm) cc_final: 0.8041 (mm) REVERT: D 709 MET cc_start: 0.8047 (ptp) cc_final: 0.7775 (ptp) outliers start: 80 outliers final: 64 residues processed: 341 average time/residue: 0.1447 time to fit residues: 83.2764 Evaluate side-chains 337 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 264 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 673 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 685 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 50 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 175 optimal weight: 0.2980 chunk 256 optimal weight: 8.9990 chunk 89 optimal weight: 0.3980 chunk 167 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 61 optimal weight: 0.0010 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** 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 = 0.4335 r_free = 0.4335 target = 0.183982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.159986 restraints weight = 39907.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.156426 restraints weight = 48468.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152174 restraints weight = 37307.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.152982 restraints weight = 34010.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.153251 restraints weight = 23751.289| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25440 Z= 0.106 Angle : 0.592 11.358 34491 Z= 0.287 Chirality : 0.041 0.286 3947 Planarity : 0.003 0.049 4309 Dihedral : 5.710 58.974 3994 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.65 % Allowed : 23.80 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 3068 helix: 1.35 (0.15), residues: 1309 sheet: -2.14 (0.27), residues: 384 loop : -1.44 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 184 TYR 0.026 0.001 TYR A 462 PHE 0.018 0.001 PHE C 315 TRP 0.019 0.001 TRP C 640 HIS 0.006 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00241 (25400) covalent geometry : angle 0.58213 (34381) SS BOND : bond 0.00248 ( 10) SS BOND : angle 1.62455 ( 20) hydrogen bonds : bond 0.03008 ( 1029) hydrogen bonds : angle 4.02303 ( 3018) link_BETA1-4 : bond 0.00549 ( 9) link_BETA1-4 : angle 1.94761 ( 27) link_NAG-ASN : bond 0.00363 ( 21) link_NAG-ASN : angle 2.17335 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 295 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 ASP cc_start: 0.7940 (t0) cc_final: 0.7573 (t0) REVERT: A 540 ILE cc_start: 0.8960 (mt) cc_final: 0.8600 (mt) REVERT: A 735 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7530 (t80) REVERT: B 280 ARG cc_start: 0.8122 (tmm-80) cc_final: 0.7918 (tmm-80) REVERT: B 340 MET cc_start: 0.7425 (tmm) cc_final: 0.6965 (ppp) REVERT: B 353 TRP cc_start: 0.7217 (OUTLIER) cc_final: 0.6612 (t60) REVERT: C 234 MET cc_start: 0.7459 (tpp) cc_final: 0.7232 (tpp) REVERT: C 400 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: C 654 ASN cc_start: 0.8722 (t0) cc_final: 0.8433 (t0) REVERT: C 768 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7924 (m) REVERT: D 50 MET cc_start: 0.7213 (tmm) cc_final: 0.6883 (tmm) REVERT: D 257 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.9037 (t) REVERT: D 298 MET cc_start: 0.7146 (mpp) cc_final: 0.6827 (mmm) REVERT: D 350 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7660 (t-90) REVERT: D 360 MET cc_start: 0.7999 (mmm) cc_final: 0.7662 (tpt) REVERT: D 709 MET cc_start: 0.7974 (ptp) cc_final: 0.7731 (ptp) REVERT: D 791 LEU cc_start: 0.7972 (mm) cc_final: 0.7635 (pp) outliers start: 71 outliers final: 57 residues processed: 355 average time/residue: 0.1448 time to fit residues: 86.2342 Evaluate side-chains 342 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 279 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 673 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 143 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 275 optimal weight: 9.9990 chunk 243 optimal weight: 0.7980 chunk 151 optimal weight: 20.0000 chunk 286 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 chunk 274 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.183832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.161497 restraints weight = 39659.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.153652 restraints weight = 45261.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.150813 restraints weight = 44758.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.151913 restraints weight = 40851.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.151972 restraints weight = 28302.870| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25440 Z= 0.112 Angle : 0.598 11.654 34491 Z= 0.290 Chirality : 0.041 0.301 3947 Planarity : 0.003 0.055 4309 Dihedral : 5.382 58.027 3986 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.54 % Allowed : 24.29 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 3068 helix: 1.38 (0.15), residues: 1308 sheet: -2.08 (0.27), residues: 389 loop : -1.45 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 184 TYR 0.016 0.001 TYR A 462 PHE 0.023 0.001 PHE B 708 TRP 0.017 0.001 TRP C 640 HIS 0.006 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00260 (25400) covalent geometry : angle 0.58801 (34381) SS BOND : bond 0.00149 ( 10) SS BOND : angle 1.62566 ( 20) hydrogen bonds : bond 0.03048 ( 1029) hydrogen bonds : angle 3.98454 ( 3018) link_BETA1-4 : bond 0.00452 ( 9) link_BETA1-4 : angle 1.93227 ( 27) link_NAG-ASN : bond 0.00330 ( 21) link_NAG-ASN : angle 2.17297 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6136 Ramachandran restraints generated. 3068 Oldfield, 0 Emsley, 3068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 288 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 HIS cc_start: 0.7481 (OUTLIER) cc_final: 0.7181 (t-90) REVERT: A 386 ASP cc_start: 0.7954 (t0) cc_final: 0.7595 (t0) REVERT: A 540 ILE cc_start: 0.8886 (mt) cc_final: 0.8518 (mt) REVERT: A 735 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7520 (t80) REVERT: B 225 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.7243 (m-70) REVERT: B 340 MET cc_start: 0.7431 (tmm) cc_final: 0.7018 (ppp) REVERT: B 353 TRP cc_start: 0.7219 (OUTLIER) cc_final: 0.6617 (t60) REVERT: C 234 MET cc_start: 0.7450 (tpp) cc_final: 0.7247 (tpp) REVERT: C 247 MET cc_start: 0.7410 (tpp) cc_final: 0.6616 (tpp) REVERT: C 400 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: C 654 ASN cc_start: 0.8728 (t0) cc_final: 0.8347 (t0) REVERT: C 768 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7924 (m) REVERT: D 50 MET cc_start: 0.7225 (tmm) cc_final: 0.6905 (tmm) REVERT: D 257 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9083 (t) REVERT: D 298 MET cc_start: 0.7172 (mpp) cc_final: 0.6848 (mmm) REVERT: D 350 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7592 (t-90) REVERT: D 360 MET cc_start: 0.8026 (mmm) cc_final: 0.7637 (tpt) REVERT: D 658 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7334 (t80) REVERT: D 709 MET cc_start: 0.8068 (ptp) cc_final: 0.7855 (ptp) REVERT: D 791 LEU cc_start: 0.7975 (mm) cc_final: 0.7648 (pp) outliers start: 68 outliers final: 56 residues processed: 343 average time/residue: 0.1576 time to fit residues: 89.3517 Evaluate side-chains 341 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 276 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 673 ASP Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 105 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 72 optimal weight: 0.0870 chunk 241 optimal weight: 3.9990 chunk 283 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 269 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 258 optimal weight: 0.0980 overall best weight: 2.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** 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 = 0.4286 r_free = 0.4286 target = 0.179281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.152704 restraints weight = 39609.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.144317 restraints weight = 42819.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.142832 restraints weight = 36945.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143663 restraints weight = 31212.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.143629 restraints weight = 24911.678| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25440 Z= 0.204 Angle : 0.660 10.888 34491 Z= 0.321 Chirality : 0.044 0.277 3947 Planarity : 0.004 0.055 4309 Dihedral : 5.672 59.059 3986 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.91 % Allowed : 24.03 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 3068 helix: 1.34 (0.15), residues: 1310 sheet: -2.20 (0.26), residues: 423 loop : -1.45 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 184 TYR 0.015 0.001 TYR A 86 PHE 0.028 0.001 PHE C 262 TRP 0.011 0.001 TRP B 564 HIS 0.007 0.001 HIS B 792 Details of bonding type rmsd covalent geometry : bond 0.00480 (25400) covalent geometry : angle 0.64995 (34381) SS BOND : bond 0.00122 ( 10) SS BOND : angle 1.46291 ( 20) hydrogen bonds : bond 0.03401 ( 1029) hydrogen bonds : angle 4.20325 ( 3018) link_BETA1-4 : bond 0.00322 ( 9) link_BETA1-4 : angle 2.03165 ( 27) link_NAG-ASN : bond 0.00426 ( 21) link_NAG-ASN : angle 2.29511 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3505.79 seconds wall clock time: 62 minutes 4.46 seconds (3724.46 seconds total)