Starting phenix.real_space_refine on Thu Mar 5 22:09:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzp_48764/03_2026/9mzp_48764.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzp_48764/03_2026/9mzp_48764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mzp_48764/03_2026/9mzp_48764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzp_48764/03_2026/9mzp_48764.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mzp_48764/03_2026/9mzp_48764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzp_48764/03_2026/9mzp_48764.map" } resolution = 3.8 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= 0.009 sd= 0.086 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 5 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: 5.91, per 1000 atoms: 0.24 Number of scatterers: 24865 At special positions: 0 Unit cell: (156.88, 101.76, 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=2.03 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: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 110 helices and 32 sheets defined 46.4% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 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: 3.913A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 4.175A 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 Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.892A 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 246 Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.658A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 Processing helix chain 'A' and resid 356 through 365 Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 4.258A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.819A 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: 3.525A pdb=" N LEU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.505A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.634A 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: 3.716A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 788 removed outlier: 4.276A pdb=" N ASP A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 removed outlier: 3.763A pdb=" N MET A 793 " --> pdb=" O GLY A 789 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU A 796 " --> pdb=" O HIS A 792 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TRP A 798 " --> pdb=" O MET A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 846 removed outlier: 6.106A pdb=" N GLY A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.868A pdb=" N ALA B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.577A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 4.324A 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: 3.526A 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 286 through 300 Processing helix chain 'B' and resid 317 through 337 removed outlier: 3.558A 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 455 through 459 removed outlier: 4.353A pdb=" N PHE B 459 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 501 through 507 removed outlier: 4.414A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.542A pdb=" N LYS B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) 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: 3.866A 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: 3.685A pdb=" N THR B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.538A pdb=" N MET B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 Processing helix chain 'B' and resid 739 through 749 Processing helix chain 'B' and resid 773 through 787 removed outlier: 4.201A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 800 removed outlier: 4.050A pdb=" N ARG B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 821 removed outlier: 4.471A pdb=" N GLY B 821 " --> pdb=" O VAL B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 844 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.510A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 removed outlier: 4.075A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 removed outlier: 3.901A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.175A pdb=" N ARG C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 246 Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.273A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 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 527 removed outlier: 3.524A 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: 4.028A 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: 4.142A pdb=" N ARG C 712 " --> pdb=" O PHE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 730 removed outlier: 4.536A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.531A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 789 removed outlier: 4.248A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 798 removed outlier: 3.592A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 796 " --> pdb=" O HIS C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 842 removed outlier: 3.703A pdb=" N PHE C 824 " --> pdb=" O ILE C 820 " (cutoff:3.500A) removed outlier: 4.125A 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: 3.718A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 4.373A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 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: 4.649A 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: 3.785A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.509A pdb=" N GLU D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 434 removed outlier: 3.613A pdb=" N SER D 432 " --> pdb=" O SER D 429 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.706A pdb=" N ASP D 507 " --> pdb=" O ARG D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 removed outlier: 3.892A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.886A 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: 4.039A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 677 removed outlier: 4.241A pdb=" N CYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 697 removed outlier: 4.085A pdb=" N THR D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.967A 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 Processing helix chain 'D' and resid 790 through 798 Processing helix chain 'D' and resid 816 through 845 removed outlier: 5.574A pdb=" N GLY D 822 " --> pdb=" O GLN D 818 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE D 824 " --> pdb=" O ILE D 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 removed outlier: 4.190A pdb=" N ALA A 105 " --> pdb=" O ARG A 37 " (cutoff:3.500A) 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 203 removed outlier: 4.915A pdb=" N HIS A 225 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE A 256 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 406 removed outlier: 4.053A 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=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 432 through 435 removed outlier: 3.663A pdb=" N VAL A 435 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA7, first strand: chain 'A' and resid 491 through 492 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: 4.025A pdb=" N PHE A 735 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 541 " --> pdb=" O PHE A 735 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 682 through 684 removed outlier: 4.025A pdb=" N PHE A 735 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 541 " --> pdb=" O PHE A 735 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 83 removed outlier: 6.309A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 105 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N HIS B 129 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 203 Processing sheet with id=AB4, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.607A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.639A 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 Processing sheet with id=AB6, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.083A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 682 through 683 removed outlier: 6.557A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 34 through 43 removed outlier: 6.017A pdb=" N HIS C 34 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR C 77 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 106 through 107 removed outlier: 6.611A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY C 382 " --> pdb=" O TYR C 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 198 through 203 removed outlier: 6.639A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C 171 " --> pdb=" O HIS C 225 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE C 227 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N PHE C 256 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU C 389 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 433 through 437 removed outlier: 3.564A pdb=" N THR C 437 " --> pdb=" O ARG C 481 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC4, first strand: chain 'C' and resid 490 through 491 removed outlier: 3.663A pdb=" N ALA C 490 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AC6, first strand: chain 'C' and resid 534 through 535 removed outlier: 3.959A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 681 through 684 removed outlier: 8.031A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 76 through 83 removed outlier: 5.786A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N PHE D 107 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY D 39 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 202 through 203 removed outlier: 6.153A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE D 256 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU D 389 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR D 404 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 369 through 370 Processing sheet with id=AD2, first strand: chain 'D' and resid 435 through 437 removed outlier: 6.578A pdb=" N VAL D 435 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD4, first strand: chain 'D' and resid 534 through 536 Processing sheet with id=AD5, first strand: chain 'D' and resid 682 through 683 removed outlier: 6.314A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 3165 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.55 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: 7800 1.34 - 1.46: 4662 1.46 - 1.58: 12700 1.58 - 1.70: 0 1.70 - 1.82: 238 Bond restraints: 25400 Sorted by residual: bond pdb=" CA ALA B 630 " pdb=" CB ALA B 630 " ideal model delta sigma weight residual 1.538 1.503 0.035 1.22e-02 6.72e+03 8.41e+00 bond pdb=" N GLU D 808 " pdb=" CA GLU D 808 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 7.00e+00 bond pdb=" N GLU D 806 " pdb=" CA GLU D 806 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.28e-02 6.10e+03 6.76e+00 bond pdb=" N VAL A 552 " pdb=" CA VAL A 552 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.24e-02 6.50e+03 6.51e+00 bond pdb=" N ILE B 473 " pdb=" CA ILE B 473 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.32e-02 5.74e+03 6.21e+00 ... (remaining 25395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.71: 34322 7.71 - 15.42: 36 15.42 - 23.13: 11 23.13 - 30.84: 5 30.84 - 38.55: 7 Bond angle restraints: 34381 Sorted by residual: angle pdb=" N LEU D 474 " pdb=" CA LEU D 474 " pdb=" C LEU D 474 " ideal model delta sigma weight residual 109.24 72.06 37.18 1.51e+00 4.39e-01 6.06e+02 angle pdb=" N GLU D 788 " pdb=" CA GLU D 788 " pdb=" C GLU D 788 " ideal model delta sigma weight residual 110.59 75.01 35.58 1.45e+00 4.76e-01 6.02e+02 angle pdb=" N LEU B 474 " pdb=" CA LEU B 474 " pdb=" C LEU B 474 " ideal model delta sigma weight residual 108.41 69.86 38.55 1.63e+00 3.76e-01 5.59e+02 angle pdb=" N LEU C 101 " pdb=" CA LEU C 101 " pdb=" C LEU C 101 " ideal model delta sigma weight residual 110.52 75.55 34.97 1.48e+00 4.57e-01 5.58e+02 angle pdb=" N GLY B 475 " pdb=" CA GLY B 475 " pdb=" C GLY B 475 " ideal model delta sigma weight residual 115.66 151.57 -35.91 1.63e+00 3.76e-01 4.85e+02 ... (remaining 34376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 13611 17.81 - 35.62: 1567 35.62 - 53.44: 313 53.44 - 71.25: 48 71.25 - 89.06: 28 Dihedral angle restraints: 15567 sinusoidal: 6623 harmonic: 8944 Sorted by residual: dihedral pdb=" C LEU A 474 " pdb=" N LEU A 474 " pdb=" CA LEU A 474 " pdb=" CB LEU A 474 " ideal model delta harmonic sigma weight residual -122.60 -89.91 -32.69 0 2.50e+00 1.60e-01 1.71e+02 dihedral pdb=" C TYR D 488 " pdb=" N TYR D 488 " pdb=" CA TYR D 488 " pdb=" CB TYR D 488 " ideal model delta harmonic sigma weight residual -122.60 -91.45 -31.15 0 2.50e+00 1.60e-01 1.55e+02 dihedral pdb=" C LEU A 101 " pdb=" N LEU A 101 " pdb=" CA LEU A 101 " pdb=" CB LEU A 101 " ideal model delta harmonic sigma weight residual -122.60 -92.27 -30.33 0 2.50e+00 1.60e-01 1.47e+02 ... (remaining 15564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 3909 0.135 - 0.270: 26 0.270 - 0.405: 4 0.405 - 0.540: 5 0.540 - 0.675: 3 Chirality restraints: 3947 Sorted by residual: chirality pdb=" CA LEU A 101 " pdb=" N LEU A 101 " pdb=" C LEU A 101 " pdb=" CB LEU A 101 " both_signs ideal model delta sigma weight residual False 2.51 3.19 -0.68 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA TYR D 488 " pdb=" N TYR D 488 " pdb=" C TYR D 488 " pdb=" CB TYR D 488 " both_signs ideal model delta sigma weight residual False 2.51 3.18 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA LEU A 474 " pdb=" N LEU A 474 " pdb=" C LEU A 474 " pdb=" CB LEU A 474 " both_signs ideal model delta sigma weight residual False 2.51 3.07 -0.56 2.00e-01 2.50e+01 7.83e+00 ... (remaining 3944 not shown) Planarity restraints: 4330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 800 " 0.576 9.50e-02 1.11e+02 2.58e-01 4.08e+01 pdb=" NE ARG A 800 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 800 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 800 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 800 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 472 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C THR B 472 " 0.055 2.00e-02 2.50e+03 pdb=" O THR B 472 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE B 473 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 169 " 0.011 2.00e-02 2.50e+03 1.35e-02 4.56e+00 pdb=" CG TRP A 169 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 169 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 169 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 169 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 169 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 169 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 169 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 169 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 169 " -0.002 2.00e-02 2.50e+03 ... (remaining 4327 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 16 2.16 - 2.85: 8607 2.85 - 3.53: 35981 3.53 - 4.22: 56728 4.22 - 4.90: 97387 Nonbonded interactions: 198719 Sorted by model distance: nonbonded pdb=" O GLN A 98 " pdb=" O LEU A 101 " model vdw 1.476 3.040 nonbonded pdb=" O LEU A 470 " pdb=" O LEU A 474 " model vdw 1.519 3.040 nonbonded pdb=" O LEU B 470 " pdb=" O LEU B 474 " model vdw 1.568 3.040 nonbonded pdb=" O GLN D 98 " pdb=" O LEU D 101 " model vdw 1.725 3.040 nonbonded pdb=" N GLU D 788 " pdb=" O GLU D 788 " model vdw 1.796 2.496 ... (remaining 198714 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.790 Find NCS groups from input model: 0.660 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 0.035 25440 Z= 0.139 Angle : 0.982 38.550 34491 Z= 0.583 Chirality : 0.050 0.675 3947 Planarity : 0.005 0.258 4309 Dihedral : 15.313 89.060 9785 Min Nonbonded Distance : 1.476 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.64 % Allowed : 13.34 % Favored : 86.02 % Cbeta Deviations : 0.42 % 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: -0.93 (0.15), residues: 3068 helix: 0.49 (0.14), residues: 1341 sheet: -1.74 (0.26), residues: 407 loop : -1.33 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 800 TYR 0.014 0.001 TYR C 462 PHE 0.023 0.001 PHE B 555 TRP 0.034 0.001 TRP A 169 HIS 0.004 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00271 (25400) covalent geometry : angle 0.97604 (34381) SS BOND : bond 0.00198 ( 10) SS BOND : angle 0.88523 ( 20) hydrogen bonds : bond 0.18208 ( 1080) hydrogen bonds : angle 6.91363 ( 3165) link_BETA1-4 : bond 0.00492 ( 9) link_BETA1-4 : angle 2.11826 ( 27) link_NAG-ASN : bond 0.00275 ( 21) link_NAG-ASN : angle 2.37882 ( 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 231 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.8137 (m-10) cc_final: 0.7666 (m-10) REVERT: A 705 MET cc_start: 0.8758 (ptp) cc_final: 0.8547 (ptp) REVERT: B 323 MET cc_start: 0.9227 (mmm) cc_final: 0.8774 (tpt) REVERT: B 360 MET cc_start: 0.8460 (tpt) cc_final: 0.7935 (tpt) REVERT: B 691 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8854 (ptt) REVERT: B 770 MET cc_start: 0.9088 (mpp) cc_final: 0.8841 (mpp) REVERT: B 792 HIS cc_start: 0.8873 (t-170) cc_final: 0.8560 (t-170) REVERT: B 796 GLU cc_start: 0.8857 (tp30) cc_final: 0.8511 (pt0) REVERT: C 360 MET cc_start: 0.9146 (tpt) cc_final: 0.8635 (tpt) REVERT: C 627 MET cc_start: 0.6481 (mpp) cc_final: 0.5920 (tmm) REVERT: C 631 LEU cc_start: 0.8928 (tp) cc_final: 0.8634 (tp) REVERT: D 196 ASN cc_start: 0.7799 (t0) cc_final: 0.7228 (t0) REVERT: D 691 MET cc_start: 0.8777 (ptt) cc_final: 0.8507 (ptt) REVERT: D 705 MET cc_start: 0.8833 (mmp) cc_final: 0.8380 (mmp) REVERT: D 806 GLU cc_start: 0.3915 (OUTLIER) cc_final: 0.3650 (pt0) outliers start: 17 outliers final: 11 residues processed: 225 average time/residue: 0.1438 time to fit residues: 54.7981 Evaluate side-chains 215 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 750 CYS Chi-restraints excluded: chain D residue 806 GLU Chi-restraints excluded: chain D residue 807 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 9.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.094395 restraints weight = 50463.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092127 restraints weight = 62562.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.093365 restraints weight = 56376.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093521 restraints weight = 41621.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093668 restraints weight = 38398.328| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25440 Z= 0.121 Angle : 0.574 9.905 34491 Z= 0.287 Chirality : 0.041 0.249 3947 Planarity : 0.004 0.050 4309 Dihedral : 6.549 68.806 3990 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.49 % Allowed : 14.24 % Favored : 84.27 % 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: -0.39 (0.15), residues: 3068 helix: 1.14 (0.14), residues: 1348 sheet: -1.64 (0.25), residues: 419 loop : -1.25 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 184 TYR 0.018 0.001 TYR A 252 PHE 0.020 0.001 PHE A 476 TRP 0.025 0.001 TRP A 169 HIS 0.007 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00266 (25400) covalent geometry : angle 0.56412 (34381) SS BOND : bond 0.00281 ( 10) SS BOND : angle 0.88942 ( 20) hydrogen bonds : bond 0.04136 ( 1080) hydrogen bonds : angle 4.74248 ( 3165) link_BETA1-4 : bond 0.00415 ( 9) link_BETA1-4 : angle 2.12117 ( 27) link_NAG-ASN : bond 0.00322 ( 21) link_NAG-ASN : angle 2.14190 ( 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 254 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.7146 (mmp) cc_final: 0.6926 (tpp) REVERT: B 323 MET cc_start: 0.8945 (mmm) cc_final: 0.8422 (tpt) REVERT: C 340 MET cc_start: 0.7394 (mmm) cc_final: 0.7122 (tpt) REVERT: C 360 MET cc_start: 0.8760 (tpt) cc_final: 0.8499 (tpt) REVERT: C 627 MET cc_start: 0.6413 (mpp) cc_final: 0.6096 (tmm) REVERT: C 631 LEU cc_start: 0.8149 (tp) cc_final: 0.7867 (tp) REVERT: D 196 ASN cc_start: 0.7250 (t0) cc_final: 0.6766 (t0) REVERT: D 536 LEU cc_start: 0.8292 (pt) cc_final: 0.7872 (pp) REVERT: D 691 MET cc_start: 0.7841 (ptt) cc_final: 0.7469 (ptt) REVERT: D 806 GLU cc_start: 0.4634 (OUTLIER) cc_final: 0.4149 (pm20) outliers start: 40 outliers final: 21 residues processed: 245 average time/residue: 0.1482 time to fit residues: 62.1425 Evaluate side-chains 218 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 334 VAL 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 B residue 827 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 750 CYS Chi-restraints excluded: chain D residue 806 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 37 optimal weight: 0.0070 chunk 290 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- 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** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.123222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.093405 restraints weight = 50963.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.091031 restraints weight = 62167.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092272 restraints weight = 58886.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092489 restraints weight = 42715.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092839 restraints weight = 38607.307| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1035 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= 0.167 Angle : 0.574 9.440 34491 Z= 0.286 Chirality : 0.041 0.228 3947 Planarity : 0.004 0.050 4309 Dihedral : 5.977 59.517 3979 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.17 % Allowed : 15.81 % Favored : 82.03 % 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: -0.34 (0.15), residues: 3068 helix: 1.30 (0.14), residues: 1344 sheet: -1.71 (0.26), residues: 393 loop : -1.34 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 663 TYR 0.023 0.001 TYR A 252 PHE 0.011 0.001 PHE A 476 TRP 0.015 0.001 TRP A 169 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00389 (25400) covalent geometry : angle 0.56431 (34381) SS BOND : bond 0.00251 ( 10) SS BOND : angle 0.78667 ( 20) hydrogen bonds : bond 0.03610 ( 1080) hydrogen bonds : angle 4.46816 ( 3165) link_BETA1-4 : bond 0.00416 ( 9) link_BETA1-4 : angle 2.14728 ( 27) link_NAG-ASN : bond 0.00324 ( 21) link_NAG-ASN : angle 2.06255 ( 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 269 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 211 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9031 (pt) REVERT: B 323 MET cc_start: 0.8881 (mmm) cc_final: 0.8555 (tpp) REVERT: B 799 TRP cc_start: 0.6164 (t-100) cc_final: 0.5835 (t-100) REVERT: C 360 MET cc_start: 0.8911 (tpt) cc_final: 0.8609 (tpt) REVERT: C 627 MET cc_start: 0.6429 (mpp) cc_final: 0.6083 (tmm) REVERT: C 631 LEU cc_start: 0.8204 (tp) cc_final: 0.7914 (tp) REVERT: D 152 ASP cc_start: 0.8037 (t0) cc_final: 0.7701 (t0) REVERT: D 196 ASN cc_start: 0.7214 (t0) cc_final: 0.6709 (t0) REVERT: D 536 LEU cc_start: 0.8492 (pt) cc_final: 0.8059 (pp) REVERT: D 806 GLU cc_start: 0.4734 (OUTLIER) cc_final: 0.3941 (pm20) outliers start: 58 outliers final: 36 residues processed: 253 average time/residue: 0.1433 time to fit residues: 62.4306 Evaluate side-chains 243 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 174 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 750 CYS Chi-restraints excluded: chain D residue 793 MET 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: 5.9990 chunk 53 optimal weight: 9.9990 chunk 131 optimal weight: 40.0000 chunk 305 optimal weight: 6.9990 chunk 236 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 262 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.120717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.090526 restraints weight = 50654.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.088335 restraints weight = 61949.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.089406 restraints weight = 61311.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089617 restraints weight = 43024.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089735 restraints weight = 39914.703| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25440 Z= 0.206 Angle : 0.597 9.644 34491 Z= 0.295 Chirality : 0.042 0.220 3947 Planarity : 0.003 0.049 4309 Dihedral : 5.775 59.913 3979 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.65 % Allowed : 17.12 % Favored : 80.23 % 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: -0.31 (0.15), residues: 3068 helix: 1.39 (0.14), residues: 1331 sheet: -1.74 (0.26), residues: 395 loop : -1.35 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 220 TYR 0.010 0.001 TYR C 252 PHE 0.022 0.001 PHE B 555 TRP 0.014 0.001 TRP D 798 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00479 (25400) covalent geometry : angle 0.58771 (34381) SS BOND : bond 0.00438 ( 10) SS BOND : angle 0.80893 ( 20) hydrogen bonds : bond 0.03476 ( 1080) hydrogen bonds : angle 4.42423 ( 3165) link_BETA1-4 : bond 0.00385 ( 9) link_BETA1-4 : angle 2.22217 ( 27) link_NAG-ASN : bond 0.00386 ( 21) link_NAG-ASN : angle 2.07071 ( 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 276 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 205 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 ASP cc_start: 0.7867 (t0) cc_final: 0.7586 (t0) REVERT: B 269 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: B 323 MET cc_start: 0.8936 (mmm) cc_final: 0.8645 (tpp) REVERT: B 555 PHE cc_start: 0.7830 (p90) cc_final: 0.7599 (p90) REVERT: B 691 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7789 (ptt) REVERT: B 799 TRP cc_start: 0.6270 (t-100) cc_final: 0.5880 (t-100) REVERT: C 360 MET cc_start: 0.8932 (tpt) cc_final: 0.8582 (tpt) REVERT: C 627 MET cc_start: 0.6385 (mpp) cc_final: 0.6063 (tmm) REVERT: C 631 LEU cc_start: 0.8177 (tp) cc_final: 0.7908 (tp) REVERT: D 685 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7778 (m) REVERT: D 806 GLU cc_start: 0.4719 (OUTLIER) cc_final: 0.3924 (pm20) outliers start: 71 outliers final: 47 residues processed: 257 average time/residue: 0.1361 time to fit residues: 60.7112 Evaluate side-chains 250 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 174 VAL Chi-restraints excluded: chain A residue 249 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 385 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 540 ILE Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 750 CYS Chi-restraints excluded: chain D residue 793 MET 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: 7.9990 chunk 50 optimal weight: 10.0000 chunk 261 optimal weight: 0.1980 chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 206 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 274 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.121552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.091900 restraints weight = 50441.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.089470 restraints weight = 62198.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090647 restraints weight = 60313.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.090852 restraints weight = 43889.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.091049 restraints weight = 39819.818| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25440 Z= 0.148 Angle : 0.570 9.443 34491 Z= 0.280 Chirality : 0.041 0.224 3947 Planarity : 0.003 0.048 4309 Dihedral : 5.559 59.002 3979 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.84 % Allowed : 18.35 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 3068 helix: 1.40 (0.14), residues: 1332 sheet: -1.66 (0.26), residues: 392 loop : -1.32 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.018 0.001 TYR A 252 PHE 0.018 0.001 PHE B 555 TRP 0.011 0.001 TRP D 353 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00345 (25400) covalent geometry : angle 0.56115 (34381) SS BOND : bond 0.00249 ( 10) SS BOND : angle 0.83548 ( 20) hydrogen bonds : bond 0.03269 ( 1080) hydrogen bonds : angle 4.30298 ( 3165) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 2.18289 ( 27) link_NAG-ASN : bond 0.00313 ( 21) link_NAG-ASN : angle 2.00723 ( 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 290 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 214 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 ASP cc_start: 0.7807 (t0) cc_final: 0.7533 (t0) REVERT: B 269 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8514 (m-80) REVERT: B 323 MET cc_start: 0.8904 (mmm) cc_final: 0.8620 (tpp) REVERT: B 331 SER cc_start: 0.8991 (p) cc_final: 0.8753 (t) REVERT: B 555 PHE cc_start: 0.7877 (p90) cc_final: 0.7647 (p90) REVERT: B 691 MET cc_start: 0.8276 (ptt) cc_final: 0.7982 (ptt) REVERT: B 784 GLN cc_start: 0.8152 (pp30) cc_final: 0.7738 (tm-30) REVERT: C 360 MET cc_start: 0.8851 (tpt) cc_final: 0.8591 (tpt) REVERT: C 627 MET cc_start: 0.6388 (mpp) cc_final: 0.6062 (tmm) REVERT: C 631 LEU cc_start: 0.8164 (tp) cc_final: 0.7892 (tp) REVERT: C 754 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8122 (pp30) REVERT: D 50 MET cc_start: 0.7726 (tmm) cc_final: 0.7410 (ttp) REVERT: D 152 ASP cc_start: 0.8021 (t0) cc_final: 0.7703 (t0) REVERT: D 196 ASN cc_start: 0.7297 (t0) cc_final: 0.6781 (t0) REVERT: D 536 LEU cc_start: 0.8437 (pt) cc_final: 0.8007 (pp) REVERT: D 806 GLU cc_start: 0.4605 (OUTLIER) cc_final: 0.3543 (pm20) outliers start: 76 outliers final: 49 residues processed: 270 average time/residue: 0.1399 time to fit residues: 65.0058 Evaluate side-chains 253 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 174 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 844 TYR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 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 750 CYS Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 750 CYS Chi-restraints excluded: chain D residue 806 GLU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 843 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 283 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 281 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 256 optimal weight: 0.6980 chunk 290 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097099 restraints weight = 50144.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093368 restraints weight = 73767.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090530 restraints weight = 55660.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.091145 restraints weight = 54320.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.091515 restraints weight = 41240.562| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25440 Z= 0.124 Angle : 0.568 12.633 34491 Z= 0.277 Chirality : 0.041 0.244 3947 Planarity : 0.003 0.048 4309 Dihedral : 5.338 57.478 3979 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.80 % Allowed : 19.06 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 3068 helix: 1.46 (0.14), residues: 1332 sheet: -1.58 (0.27), residues: 392 loop : -1.30 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.013 0.001 TYR A 252 PHE 0.017 0.001 PHE B 744 TRP 0.012 0.001 TRP B 799 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00288 (25400) covalent geometry : angle 0.55910 (34381) SS BOND : bond 0.00225 ( 10) SS BOND : angle 0.79851 ( 20) hydrogen bonds : bond 0.03122 ( 1080) hydrogen bonds : angle 4.18944 ( 3165) link_BETA1-4 : bond 0.00487 ( 9) link_BETA1-4 : angle 2.17746 ( 27) link_NAG-ASN : bond 0.00278 ( 21) link_NAG-ASN : angle 1.97917 ( 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 286 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 211 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 467 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8932 (tt) REVERT: B 152 ASP cc_start: 0.7882 (t0) cc_final: 0.7491 (t0) REVERT: B 269 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: B 323 MET cc_start: 0.8886 (mmm) cc_final: 0.8601 (tpp) REVERT: B 331 SER cc_start: 0.9015 (p) cc_final: 0.8801 (t) REVERT: B 784 GLN cc_start: 0.8137 (pp30) cc_final: 0.7645 (tm-30) REVERT: C 627 MET cc_start: 0.6450 (mpp) cc_final: 0.6108 (tmm) REVERT: C 631 LEU cc_start: 0.8226 (tp) cc_final: 0.7960 (tp) REVERT: C 754 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8134 (pp30) REVERT: D 50 MET cc_start: 0.7627 (tmm) cc_final: 0.7422 (ttp) REVERT: D 152 ASP cc_start: 0.8044 (t0) cc_final: 0.7696 (t0) REVERT: D 196 ASN cc_start: 0.7307 (t0) cc_final: 0.6791 (t0) REVERT: D 380 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8768 (m) REVERT: D 536 LEU cc_start: 0.8411 (pt) cc_final: 0.7999 (pp) REVERT: D 691 MET cc_start: 0.7846 (ptt) cc_final: 0.7537 (ptt) REVERT: D 806 GLU cc_start: 0.4734 (OUTLIER) cc_final: 0.3801 (pm20) outliers start: 75 outliers final: 45 residues processed: 269 average time/residue: 0.1396 time to fit residues: 64.8632 Evaluate side-chains 250 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 174 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 750 CYS Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 806 GLU Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 843 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 78 optimal weight: 6.9990 chunk 258 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 201 optimal weight: 0.0270 chunk 123 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 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 = 0.3811 r_free = 0.3811 target = 0.122418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.092352 restraints weight = 50491.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090218 restraints weight = 66562.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091309 restraints weight = 60886.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.091568 restraints weight = 43127.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.091755 restraints weight = 39804.899| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25440 Z= 0.128 Angle : 0.579 11.934 34491 Z= 0.283 Chirality : 0.041 0.239 3947 Planarity : 0.003 0.048 4309 Dihedral : 5.197 58.936 3978 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.62 % Allowed : 19.62 % Favored : 77.77 % 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: -0.19 (0.16), residues: 3068 helix: 1.45 (0.14), residues: 1337 sheet: -1.56 (0.27), residues: 392 loop : -1.29 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.013 0.001 TYR A 252 PHE 0.020 0.001 PHE A 166 TRP 0.011 0.001 TRP B 799 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00299 (25400) covalent geometry : angle 0.57025 (34381) SS BOND : bond 0.00225 ( 10) SS BOND : angle 0.69993 ( 20) hydrogen bonds : bond 0.03103 ( 1080) hydrogen bonds : angle 4.18222 ( 3165) link_BETA1-4 : bond 0.00515 ( 9) link_BETA1-4 : angle 2.16916 ( 27) link_NAG-ASN : bond 0.00280 ( 21) link_NAG-ASN : angle 1.96197 ( 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 282 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 212 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 467 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8849 (tt) REVERT: B 152 ASP cc_start: 0.7841 (t0) cc_final: 0.7535 (t0) REVERT: B 269 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8573 (m-80) REVERT: B 323 MET cc_start: 0.8862 (mmm) cc_final: 0.8591 (tpp) REVERT: B 331 SER cc_start: 0.8976 (p) cc_final: 0.8773 (t) REVERT: B 691 MET cc_start: 0.8002 (ptt) cc_final: 0.7660 (ptt) REVERT: B 725 ILE cc_start: 0.8973 (mm) cc_final: 0.8763 (mm) REVERT: B 784 GLN cc_start: 0.8026 (pp30) cc_final: 0.7580 (tm-30) REVERT: C 627 MET cc_start: 0.6444 (mpp) cc_final: 0.6120 (tmm) REVERT: C 631 LEU cc_start: 0.8116 (tp) cc_final: 0.7859 (tp) REVERT: C 754 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8118 (pp30) REVERT: D 50 MET cc_start: 0.7657 (tmm) cc_final: 0.7453 (ttp) REVERT: D 152 ASP cc_start: 0.7994 (t0) cc_final: 0.7681 (t0) REVERT: D 180 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8711 (m) REVERT: D 196 ASN cc_start: 0.7385 (t0) cc_final: 0.6830 (t0) REVERT: D 380 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8732 (m) REVERT: D 536 LEU cc_start: 0.8393 (pt) cc_final: 0.7957 (pp) REVERT: D 705 MET cc_start: 0.7248 (mmp) cc_final: 0.6990 (mmp) outliers start: 70 outliers final: 50 residues processed: 265 average time/residue: 0.1405 time to fit residues: 64.3587 Evaluate side-chains 261 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 174 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 302 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 750 CYS Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 827 LEU Chi-restraints excluded: chain D residue 843 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 143 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** D 137 GLN D 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.121439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.091295 restraints weight = 50495.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.089286 restraints weight = 61769.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090326 restraints weight = 57132.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090453 restraints weight = 42529.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.090612 restraints weight = 38885.409| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25440 Z= 0.167 Angle : 0.610 12.968 34491 Z= 0.299 Chirality : 0.042 0.229 3947 Planarity : 0.003 0.048 4309 Dihedral : 5.145 59.638 3975 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.77 % Allowed : 19.69 % Favored : 77.54 % 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: -0.19 (0.16), residues: 3068 helix: 1.44 (0.14), residues: 1341 sheet: -1.61 (0.27), residues: 380 loop : -1.29 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 663 TYR 0.016 0.001 TYR C 651 PHE 0.027 0.001 PHE A 166 TRP 0.014 0.001 TRP D 798 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00391 (25400) covalent geometry : angle 0.59895 (34381) SS BOND : bond 0.00213 ( 10) SS BOND : angle 2.38206 ( 20) hydrogen bonds : bond 0.03215 ( 1080) hydrogen bonds : angle 4.24253 ( 3165) link_BETA1-4 : bond 0.00416 ( 9) link_BETA1-4 : angle 2.14738 ( 27) link_NAG-ASN : bond 0.00321 ( 21) link_NAG-ASN : angle 1.99770 ( 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 278 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 204 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 467 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8890 (tt) REVERT: B 152 ASP cc_start: 0.7785 (t0) cc_final: 0.7472 (t0) REVERT: B 269 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8590 (m-80) REVERT: B 323 MET cc_start: 0.8884 (mmm) cc_final: 0.8596 (tpp) REVERT: B 331 SER cc_start: 0.9005 (p) cc_final: 0.8766 (t) REVERT: B 360 MET cc_start: 0.8452 (tpt) cc_final: 0.7771 (tpt) REVERT: B 691 MET cc_start: 0.8141 (ptt) cc_final: 0.7856 (ptt) REVERT: B 725 ILE cc_start: 0.9039 (mm) cc_final: 0.8826 (mm) REVERT: C 627 MET cc_start: 0.6442 (mpp) cc_final: 0.6110 (tmm) REVERT: C 631 LEU cc_start: 0.8129 (tp) cc_final: 0.7869 (tp) REVERT: C 754 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8142 (pp30) REVERT: C 764 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: D 50 MET cc_start: 0.7659 (tmm) cc_final: 0.7455 (ttp) REVERT: D 152 ASP cc_start: 0.8084 (t0) cc_final: 0.7727 (t0) REVERT: D 196 ASN cc_start: 0.7297 (t0) cc_final: 0.6783 (t0) REVERT: D 360 MET cc_start: 0.8509 (tpt) cc_final: 0.7661 (tpt) REVERT: D 380 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8726 (m) REVERT: D 536 LEU cc_start: 0.8488 (pt) cc_final: 0.8063 (pp) REVERT: D 691 MET cc_start: 0.7812 (ptt) cc_final: 0.7516 (ptt) REVERT: D 705 MET cc_start: 0.7277 (mmp) cc_final: 0.7026 (mmp) outliers start: 74 outliers final: 54 residues processed: 263 average time/residue: 0.1360 time to fit residues: 61.8010 Evaluate side-chains 262 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 174 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 750 CYS Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 764 TYR Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 ILE 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 274 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 721 ASN Chi-restraints excluded: chain D residue 827 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 50 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 249 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 143 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.123318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.093655 restraints weight = 50377.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.091579 restraints weight = 58293.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092622 restraints weight = 57167.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092854 restraints weight = 42169.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093086 restraints weight = 37966.185| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1568 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= 0.110 Angle : 0.597 11.932 34491 Z= 0.290 Chirality : 0.041 0.239 3947 Planarity : 0.003 0.048 4309 Dihedral : 5.011 59.417 3975 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.06 % Allowed : 20.52 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.16), residues: 3068 helix: 1.42 (0.14), residues: 1343 sheet: -1.54 (0.27), residues: 379 loop : -1.25 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 663 TYR 0.015 0.001 TYR B 86 PHE 0.029 0.001 PHE A 166 TRP 0.013 0.001 TRP B 799 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00253 (25400) covalent geometry : angle 0.58747 (34381) SS BOND : bond 0.00180 ( 10) SS BOND : angle 1.87994 ( 20) hydrogen bonds : bond 0.03046 ( 1080) hydrogen bonds : angle 4.15727 ( 3165) link_BETA1-4 : bond 0.00554 ( 9) link_BETA1-4 : angle 2.11329 ( 27) link_NAG-ASN : bond 0.00288 ( 21) link_NAG-ASN : angle 1.92335 ( 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 267 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 212 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 384 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8871 (ptm160) REVERT: B 152 ASP cc_start: 0.7896 (t0) cc_final: 0.7465 (t0) REVERT: B 269 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: B 323 MET cc_start: 0.8928 (mmm) cc_final: 0.8635 (tpp) REVERT: B 360 MET cc_start: 0.8499 (tpt) cc_final: 0.7812 (tpt) REVERT: B 691 MET cc_start: 0.8347 (ptt) cc_final: 0.8043 (ptt) REVERT: C 627 MET cc_start: 0.6423 (mpp) cc_final: 0.6091 (tmm) REVERT: C 631 LEU cc_start: 0.8212 (tp) cc_final: 0.7953 (tp) REVERT: C 754 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8227 (pp30) REVERT: C 764 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: D 152 ASP cc_start: 0.8015 (t0) cc_final: 0.7673 (t0) REVERT: D 196 ASN cc_start: 0.7363 (t0) cc_final: 0.6844 (t0) REVERT: D 360 MET cc_start: 0.8546 (tpt) cc_final: 0.7678 (tpt) REVERT: D 380 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8795 (m) REVERT: D 536 LEU cc_start: 0.8419 (pt) cc_final: 0.7963 (pp) REVERT: D 691 MET cc_start: 0.8006 (ptt) cc_final: 0.7684 (ptt) REVERT: D 705 MET cc_start: 0.7359 (mmp) cc_final: 0.7103 (mmp) outliers start: 55 outliers final: 43 residues processed: 252 average time/residue: 0.1427 time to fit residues: 61.6284 Evaluate side-chains 254 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 174 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 302 GLN Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 750 CYS Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 764 TYR Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 685 VAL Chi-restraints excluded: chain D residue 721 ASN 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: 0.9990 chunk 62 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 275 optimal weight: 6.9990 chunk 243 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 274 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** D 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.123431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.093784 restraints weight = 50148.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.091810 restraints weight = 60179.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092886 restraints weight = 57930.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.093091 restraints weight = 41661.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093267 restraints weight = 38043.298| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25440 Z= 0.117 Angle : 0.616 16.781 34491 Z= 0.298 Chirality : 0.041 0.238 3947 Planarity : 0.003 0.073 4309 Dihedral : 4.953 59.461 3972 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.02 % Allowed : 20.74 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.16), residues: 3068 helix: 1.41 (0.14), residues: 1344 sheet: -1.51 (0.27), residues: 380 loop : -1.25 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 800 TYR 0.017 0.001 TYR B 86 PHE 0.037 0.001 PHE C 555 TRP 0.012 0.001 TRP B 799 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00269 (25400) covalent geometry : angle 0.60710 (34381) SS BOND : bond 0.00223 ( 10) SS BOND : angle 1.60828 ( 20) hydrogen bonds : bond 0.03062 ( 1080) hydrogen bonds : angle 4.15994 ( 3165) link_BETA1-4 : bond 0.00525 ( 9) link_BETA1-4 : angle 2.09702 ( 27) link_NAG-ASN : bond 0.00283 ( 21) link_NAG-ASN : angle 1.93520 ( 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 263 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 384 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8857 (ptm160) REVERT: B 152 ASP cc_start: 0.7856 (t0) cc_final: 0.7545 (t0) REVERT: B 269 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: B 323 MET cc_start: 0.8917 (mmm) cc_final: 0.8639 (tpp) REVERT: B 691 MET cc_start: 0.8334 (ptt) cc_final: 0.8025 (ptt) REVERT: C 627 MET cc_start: 0.6417 (mpp) cc_final: 0.6091 (tmm) REVERT: C 631 LEU cc_start: 0.8204 (tp) cc_final: 0.7949 (tp) REVERT: C 754 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8227 (pp30) REVERT: C 764 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: D 152 ASP cc_start: 0.7969 (t0) cc_final: 0.7635 (t0) REVERT: D 196 ASN cc_start: 0.7335 (t0) cc_final: 0.6813 (t0) REVERT: D 380 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8804 (m) REVERT: D 536 LEU cc_start: 0.8415 (pt) cc_final: 0.7966 (pp) REVERT: D 691 MET cc_start: 0.8006 (ptt) cc_final: 0.7688 (ptt) REVERT: D 705 MET cc_start: 0.7327 (mmp) cc_final: 0.7076 (mmp) outliers start: 54 outliers final: 45 residues processed: 246 average time/residue: 0.1302 time to fit residues: 55.5783 Evaluate side-chains 256 residues out of total 2676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 174 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 750 CYS Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 750 CYS Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 764 TYR Chi-restraints excluded: chain C residue 817 VAL Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 658 PHE 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: 0.7980 chunk 107 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 217 optimal weight: 0.0170 chunk 72 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 283 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 269 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 overall best weight: 0.9420 ------------------------------------------------------------------------------- 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** D 721 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.123838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094460 restraints weight = 50218.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092345 restraints weight = 64638.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.093657 restraints weight = 57562.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.093796 restraints weight = 40834.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.094007 restraints weight = 38629.793| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25440 Z= 0.115 Angle : 0.612 13.103 34491 Z= 0.295 Chirality : 0.041 0.289 3947 Planarity : 0.003 0.048 4309 Dihedral : 4.857 58.696 3972 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.20 % Allowed : 20.55 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 3068 helix: 1.42 (0.14), residues: 1340 sheet: -1.54 (0.27), residues: 393 loop : -1.24 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 800 TYR 0.015 0.001 TYR B 86 PHE 0.020 0.001 PHE C 337 TRP 0.017 0.001 TRP B 799 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00265 (25400) covalent geometry : angle 0.60374 (34381) SS BOND : bond 0.00189 ( 10) SS BOND : angle 1.38993 ( 20) hydrogen bonds : bond 0.03044 ( 1080) hydrogen bonds : angle 4.12118 ( 3165) link_BETA1-4 : bond 0.00493 ( 9) link_BETA1-4 : angle 2.05595 ( 27) link_NAG-ASN : bond 0.00255 ( 21) link_NAG-ASN : angle 1.95302 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3398.65 seconds wall clock time: 60 minutes 11.42 seconds (3611.42 seconds total)