Starting phenix.real_space_refine on Mon Aug 25 15:21:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f38_28833/08_2025/8f38_28833_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f38_28833/08_2025/8f38_28833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f38_28833/08_2025/8f38_28833_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f38_28833/08_2025/8f38_28833_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f38_28833/08_2025/8f38_28833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f38_28833/08_2025/8f38_28833.map" } resolution = 2.64 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= -0.001 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14871 atoms to isotropic. 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 81 5.16 5 C 10644 2.51 5 N 2829 2.21 5 O 3398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16952 Number of models: 1 Model: "" Number of chains: 21 Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 901 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} bond proxies already assigned to first conformer: 917 Chain: "E" Number of atoms: 901 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} bond proxies already assigned to first conformer: 917 Chain: "F" Number of atoms: 901 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} bond proxies already assigned to first conformer: 917 Chain: "A" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3799 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 21, 'TRANS': 458} Chain breaks: 1 Chain: "B" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3799 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 21, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3799 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 21, 'TRANS': 458} Chain breaks: 1 Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 783 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 4.21, per 1000 atoms: 0.25 Number of scatterers: 16952 At special positions: 0 Unit cell: (135, 127.575, 143.1, 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 81 16.00 O 3398 8.00 N 2829 7.00 C 10644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 480 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 84 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 319 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 480 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 295 " - pdb=" SG CYS C 319 " distance=2.03 Simple disulfide: pdb=" SG CYS C 487 " - pdb=" SG CYS C 491 " 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 Atom "HETATM16567 O5 NAG M 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 28 " " NAG A 602 " - " ASN A 142 " " NAG A 603 " - " ASN A 303 " " NAG A 604 " - " ASN A 497 " " NAG A 605 " - " ASN A 71 " " NAG A 606 " - " ASN A 176 " " NAG B 601 " - " ASN B 28 " " NAG B 602 " - " ASN B 142 " " NAG B 603 " - " ASN B 303 " " NAG B 604 " - " ASN B 497 " " NAG B 605 " - " ASN B 71 " " NAG B 606 " - " ASN B 176 " " NAG C 601 " - " ASN C 142 " " NAG C 602 " - " ASN C 303 " " NAG C 603 " - " ASN C 497 " " NAG C 604 " - " ASN C 71 " " NAG C 605 " - " ASN C 176 " " NAG C 606 " - " ASN C 28 " " NAG J 1 " - " ASN A 40 " " NAG K 1 " - " ASN A 104 " " NAG L 1 " - " ASN B 104 " " NAG M 1 " - " ASN B 40 " " NAG N 1 " - " ASN C 104 " " NAG O 1 " - " ASN C 40 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 711.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 54 sheets defined 18.4% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.754A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.735A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.744A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'A' and resid 380 through 402 removed outlier: 3.676A pdb=" N THR A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 470 removed outlier: 3.954A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.847A pdb=" N TYR A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 114 through 123 Processing helix chain 'B' and resid 200 through 209 Processing helix chain 'B' and resid 380 through 402 removed outlier: 3.675A pdb=" N THR B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 470 removed outlier: 3.954A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 451 " --> pdb=" O ASN B 447 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B 468 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.847A pdb=" N TYR B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 80 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 380 through 402 removed outlier: 3.675A pdb=" N THR C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET C 402 " --> pdb=" O VAL C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 470 removed outlier: 3.954A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 451 " --> pdb=" O ASN C 447 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN C 468 " --> pdb=" O LYS C 464 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 501 through 506 removed outlier: 3.847A pdb=" N TYR C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.438A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AA3, first strand: chain 'G' and resid 17 through 20 Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.627A pdb=" N ILE D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.825A pdb=" N VAL D 110 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.620A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.820A pdb=" N VAL E 110 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.613A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.816A pdb=" N VAL F 110 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 374 through 379 Processing sheet with id=AB5, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AB6, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AB7, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AB8, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.436A pdb=" N LEU A 58 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS A 291 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.539A pdb=" N LEU A 67 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 96 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER A 127 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A 269 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU A 192 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 271 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU A 192 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER A 127 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A 269 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU A 192 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 271 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AC4, first strand: chain 'A' and resid 149 through 154 removed outlier: 4.721A pdb=" N CYS A 152 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 177 through 182 Processing sheet with id=AC6, first strand: chain 'A' and resid 301 through 302 removed outlier: 3.895A pdb=" N CYS A 295 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 379 Processing sheet with id=AC8, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=AC9, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AD1, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AD2, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.436A pdb=" N LEU B 58 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N CYS B 291 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.539A pdb=" N LEU B 67 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 96 " --> pdb=" O ILE B 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER B 127 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR B 269 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 192 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 271 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU B 192 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER B 127 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR B 269 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 192 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 271 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AD7, first strand: chain 'B' and resid 149 through 154 removed outlier: 4.721A pdb=" N CYS B 152 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 177 through 182 Processing sheet with id=AD9, first strand: chain 'B' and resid 301 through 302 removed outlier: 3.895A pdb=" N CYS B 295 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 374 through 379 Processing sheet with id=AE2, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AE3, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AE5, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.435A pdb=" N LEU C 58 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS C 291 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.539A pdb=" N LEU C 67 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE C 96 " --> pdb=" O ILE C 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER C 127 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 269 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 192 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 271 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU C 192 " --> pdb=" O PRO C 267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 125 through 132 removed outlier: 3.605A pdb=" N SER C 127 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR C 269 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU C 192 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 271 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AF1, first strand: chain 'C' and resid 149 through 154 removed outlier: 4.720A pdb=" N CYS C 152 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 177 through 182 Processing sheet with id=AF3, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.895A pdb=" N CYS C 295 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 9 through 12 removed outlier: 6.438A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AF6, first strand: chain 'H' and resid 17 through 20 Processing sheet with id=AF7, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.438A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 9 through 12 Processing sheet with id=AF9, first strand: chain 'I' and resid 17 through 20 684 hydrogen bonds defined for protein. 1809 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: 2.19 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3209 1.33 - 1.45: 4698 1.45 - 1.58: 9286 1.58 - 1.70: 0 1.70 - 1.83: 114 Bond restraints: 17307 Sorted by residual: bond pdb=" C CYS C 291 " pdb=" O CYS C 291 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.28e-02 6.10e+03 6.38e+00 bond pdb=" C CYS A 291 " pdb=" O CYS A 291 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.28e-02 6.10e+03 6.26e+00 bond pdb=" C CYS B 291 " pdb=" O CYS B 291 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.28e-02 6.10e+03 6.22e+00 bond pdb=" N CYS H 22 " pdb=" CA CYS H 22 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.67e+00 bond pdb=" N SER H 23 " pdb=" CA SER H 23 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.20e-02 6.94e+03 4.64e+00 ... (remaining 17302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 22327 1.24 - 2.47: 940 2.47 - 3.71: 204 3.71 - 4.95: 28 4.95 - 6.18: 15 Bond angle restraints: 23514 Sorted by residual: angle pdb=" C GLU C 290 " pdb=" N CYS C 291 " pdb=" CA CYS C 291 " ideal model delta sigma weight residual 122.02 116.04 5.98 1.89e+00 2.80e-01 1.00e+01 angle pdb=" C GLU A 290 " pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta sigma weight residual 122.02 116.05 5.97 1.89e+00 2.80e-01 9.96e+00 angle pdb=" C GLU B 290 " pdb=" N CYS B 291 " pdb=" CA CYS B 291 " ideal model delta sigma weight residual 122.02 116.06 5.96 1.89e+00 2.80e-01 9.93e+00 angle pdb=" O GLU C 290 " pdb=" C GLU C 290 " pdb=" N CYS C 291 " ideal model delta sigma weight residual 122.19 118.21 3.98 1.29e+00 6.01e-01 9.54e+00 angle pdb=" O GLU A 290 " pdb=" C GLU A 290 " pdb=" N CYS A 291 " ideal model delta sigma weight residual 122.19 118.21 3.98 1.29e+00 6.01e-01 9.53e+00 ... (remaining 23509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 9451 21.58 - 43.15: 912 43.15 - 64.73: 229 64.73 - 86.30: 70 86.30 - 107.88: 30 Dihedral angle restraints: 10692 sinusoidal: 4605 harmonic: 6087 Sorted by residual: dihedral pdb=" CB CYS B 487 " pdb=" SG CYS B 487 " pdb=" SG CYS B 491 " pdb=" CB CYS B 491 " ideal model delta sinusoidal sigma weight residual -86.00 -33.91 -52.09 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS A 487 " pdb=" SG CYS A 487 " pdb=" SG CYS A 491 " pdb=" CB CYS A 491 " ideal model delta sinusoidal sigma weight residual -86.00 -33.95 -52.05 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS C 487 " pdb=" SG CYS C 487 " pdb=" SG CYS C 491 " pdb=" CB CYS C 491 " ideal model delta sinusoidal sigma weight residual -86.00 -33.97 -52.03 1 1.00e+01 1.00e-02 3.69e+01 ... (remaining 10689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2559 0.106 - 0.211: 68 0.211 - 0.317: 8 0.317 - 0.423: 3 0.423 - 0.528: 2 Chirality restraints: 2640 Sorted by residual: chirality pdb=" C1 NAG B 606 " pdb=" ND2 ASN B 176 " pdb=" C2 NAG B 606 " pdb=" O5 NAG B 606 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C 40 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.90 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 142 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 2637 not shown) Planarity restraints: 3027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 176 " -0.160 2.00e-02 2.50e+03 1.57e-01 3.09e+02 pdb=" CG ASN B 176 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN B 176 " 0.072 2.00e-02 2.50e+03 pdb=" ND2 ASN B 176 " 0.221 2.00e-02 2.50e+03 pdb=" C1 NAG B 606 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 40 " 0.156 2.00e-02 2.50e+03 1.45e-01 2.61e+02 pdb=" CG ASN B 40 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN B 40 " -0.093 2.00e-02 2.50e+03 pdb=" ND2 ASN B 40 " -0.174 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 40 " -0.095 2.00e-02 2.50e+03 8.45e-02 8.93e+01 pdb=" CG ASN C 40 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN C 40 " 0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN C 40 " 0.104 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.106 2.00e-02 2.50e+03 ... (remaining 3024 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 499 2.70 - 3.25: 14295 3.25 - 3.80: 24846 3.80 - 4.35: 34185 4.35 - 4.90: 59293 Nonbonded interactions: 133118 Sorted by model distance: nonbonded pdb=" OD1 ASN C 176 " pdb=" C1 NAG C 605 " model vdw 2.148 2.776 nonbonded pdb=" OD1 ASN B 40 " pdb=" C1 NAG M 1 " model vdw 2.225 2.776 nonbonded pdb=" O GLY C 355 " pdb=" O HOH C 701 " model vdw 2.240 3.040 nonbonded pdb=" ND2 ASN B 176 " pdb=" N2 NAG B 606 " model vdw 2.257 2.560 nonbonded pdb=" O GLY A 355 " pdb=" O HOH A 701 " model vdw 2.262 3.040 ... (remaining 133113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 29 or resid 31 through 119)) selection = (chain 'E' and (resid 2 through 29 or resid 31 through 119)) selection = (chain 'F' and (resid 2 through 29 or resid 31 through 119)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.920 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.005 0.240 17358 Z= 0.240 Angle : 0.797 33.261 23649 Z= 0.362 Chirality : 0.049 0.528 2640 Planarity : 0.005 0.078 3003 Dihedral : 19.167 107.878 6774 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.29 % Favored : 97.42 % Rotamer: Outliers : 4.08 % Allowed : 24.85 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.18), residues: 2100 helix: 2.55 (0.29), residues: 318 sheet: 0.73 (0.21), residues: 615 loop : -0.94 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 162 TYR 0.012 0.001 TYR I 99 PHE 0.013 0.001 PHE A 453 TRP 0.008 0.001 TRP B 435 HIS 0.005 0.001 HIS A 369 Details of bonding type rmsd covalent geometry : bond 0.00350 (17307) covalent geometry : angle 0.60285 (23514) SS BOND : bond 0.00305 ( 18) SS BOND : angle 0.84495 ( 36) hydrogen bonds : bond 0.14811 ( 633) hydrogen bonds : angle 6.77406 ( 1809) link_BETA1-4 : bond 0.00509 ( 9) link_BETA1-4 : angle 1.66727 ( 27) link_NAG-ASN : bond 0.08691 ( 24) link_NAG-ASN : angle 9.41458 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 0.497 Fit side-chains REVERT: G 5 THR cc_start: 0.6825 (OUTLIER) cc_final: 0.6409 (p) REVERT: D 74 ASP cc_start: 0.8252 (m-30) cc_final: 0.8017 (m-30) REVERT: A 162 ARG cc_start: 0.8278 (mpt180) cc_final: 0.8053 (mpt90) REVERT: A 400 GLU cc_start: 0.7969 (tt0) cc_final: 0.7665 (tt0) REVERT: A 459 LYS cc_start: 0.8181 (tttm) cc_final: 0.7730 (tttt) REVERT: B 162 ARG cc_start: 0.8310 (mpt180) cc_final: 0.8067 (mpt90) REVERT: B 400 GLU cc_start: 0.8070 (tt0) cc_final: 0.7808 (tt0) REVERT: B 403 ASN cc_start: 0.7258 (m-40) cc_final: 0.6965 (m-40) REVERT: B 420 MET cc_start: 0.7958 (ttm) cc_final: 0.7585 (mmm) REVERT: B 459 LYS cc_start: 0.8071 (tttm) cc_final: 0.7630 (tttt) REVERT: C 64 ILE cc_start: 0.8550 (mt) cc_final: 0.8173 (mt) REVERT: C 162 ARG cc_start: 0.8297 (mpt180) cc_final: 0.8059 (mpt90) REVERT: C 370 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7339 (tp-100) REVERT: C 381 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7361 (tm-30) REVERT: C 400 GLU cc_start: 0.8047 (tt0) cc_final: 0.7755 (tt0) REVERT: C 459 LYS cc_start: 0.8143 (tttm) cc_final: 0.7714 (tttt) REVERT: H 5 THR cc_start: 0.6892 (OUTLIER) cc_final: 0.6610 (p) REVERT: I 5 THR cc_start: 0.6572 (OUTLIER) cc_final: 0.6115 (p) outliers start: 67 outliers final: 46 residues processed: 262 average time/residue: 0.4633 time to fit residues: 136.1528 Evaluate side-chains 225 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.150557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.113067 restraints weight = 17746.241| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.51 r_work: 0.2985 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17358 Z= 0.149 Angle : 0.624 7.837 23649 Z= 0.317 Chirality : 0.047 0.343 2640 Planarity : 0.005 0.059 3003 Dihedral : 11.199 68.856 3050 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.29 % Favored : 97.57 % Rotamer: Outliers : 4.91 % Allowed : 22.39 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.18), residues: 2100 helix: 2.45 (0.28), residues: 330 sheet: 0.91 (0.21), residues: 612 loop : -0.89 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 87 TYR 0.013 0.002 TYR I 99 PHE 0.018 0.002 PHE A 128 TRP 0.008 0.001 TRP C 435 HIS 0.004 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00333 (17307) covalent geometry : angle 0.60525 (23514) SS BOND : bond 0.00528 ( 18) SS BOND : angle 1.54073 ( 36) hydrogen bonds : bond 0.06684 ( 633) hydrogen bonds : angle 5.04230 ( 1809) link_BETA1-4 : bond 0.00520 ( 9) link_BETA1-4 : angle 2.01278 ( 27) link_NAG-ASN : bond 0.00338 ( 24) link_NAG-ASN : angle 2.38903 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 181 time to evaluate : 0.707 Fit side-chains REVERT: D 74 ASP cc_start: 0.8499 (m-30) cc_final: 0.8253 (m-30) REVERT: F 63 LYS cc_start: 0.7699 (ttpt) cc_final: 0.7354 (ttmm) REVERT: A 22 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8906 (mt) REVERT: A 162 ARG cc_start: 0.8842 (mpt180) cc_final: 0.8556 (mpt90) REVERT: A 400 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8202 (tt0) REVERT: A 403 ASN cc_start: 0.7489 (m-40) cc_final: 0.7209 (m-40) REVERT: A 459 LYS cc_start: 0.8592 (tttm) cc_final: 0.8245 (tttt) REVERT: B 162 ARG cc_start: 0.8869 (mpt180) cc_final: 0.8595 (mpt90) REVERT: B 400 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8294 (tt0) REVERT: B 403 ASN cc_start: 0.7444 (m-40) cc_final: 0.7140 (m-40) REVERT: B 459 LYS cc_start: 0.8504 (tttm) cc_final: 0.8157 (tttt) REVERT: C 64 ILE cc_start: 0.8700 (mt) cc_final: 0.8363 (mt) REVERT: C 299 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8683 (mm-40) REVERT: C 370 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7346 (tp-100) REVERT: C 400 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8295 (tt0) REVERT: C 459 LYS cc_start: 0.8524 (tttm) cc_final: 0.8183 (tttt) REVERT: I 19 THR cc_start: 0.5544 (OUTLIER) cc_final: 0.5280 (t) outliers start: 82 outliers final: 36 residues processed: 242 average time/residue: 0.5695 time to fit residues: 153.5101 Evaluate side-chains 211 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 114 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 90 optimal weight: 0.0030 chunk 72 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.158479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122953 restraints weight = 19329.121| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.34 r_work: 0.3235 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17358 Z= 0.126 Angle : 0.577 8.489 23649 Z= 0.293 Chirality : 0.045 0.336 2640 Planarity : 0.005 0.054 3003 Dihedral : 7.967 55.709 3011 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.29 % Favored : 97.57 % Rotamer: Outliers : 4.41 % Allowed : 23.12 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.18), residues: 2100 helix: 2.64 (0.28), residues: 330 sheet: 1.11 (0.21), residues: 606 loop : -0.82 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 87 TYR 0.013 0.001 TYR I 99 PHE 0.017 0.002 PHE A 128 TRP 0.009 0.001 TRP C 435 HIS 0.004 0.001 HIS B 369 Details of bonding type rmsd covalent geometry : bond 0.00272 (17307) covalent geometry : angle 0.55812 (23514) SS BOND : bond 0.00456 ( 18) SS BOND : angle 1.32224 ( 36) hydrogen bonds : bond 0.06199 ( 633) hydrogen bonds : angle 4.76725 ( 1809) link_BETA1-4 : bond 0.00579 ( 9) link_BETA1-4 : angle 2.23342 ( 27) link_NAG-ASN : bond 0.00416 ( 24) link_NAG-ASN : angle 2.19452 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 178 time to evaluate : 0.558 Fit side-chains REVERT: G 52 ASN cc_start: 0.6316 (OUTLIER) cc_final: 0.6008 (t160) REVERT: D 74 ASP cc_start: 0.8532 (m-30) cc_final: 0.8289 (m-30) REVERT: F 63 LYS cc_start: 0.7705 (ttpt) cc_final: 0.7381 (ttmm) REVERT: A 162 ARG cc_start: 0.8841 (mpt180) cc_final: 0.8599 (mpt90) REVERT: A 232 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7471 (tptm) REVERT: A 400 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: A 459 LYS cc_start: 0.8602 (tttm) cc_final: 0.8270 (tttt) REVERT: B 162 ARG cc_start: 0.8831 (mpt180) cc_final: 0.8599 (mpt90) REVERT: B 400 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: B 403 ASN cc_start: 0.7352 (m-40) cc_final: 0.7129 (m-40) REVERT: B 420 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8332 (mmm) REVERT: B 459 LYS cc_start: 0.8504 (tttm) cc_final: 0.8173 (tttt) REVERT: C 22 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8781 (mm) REVERT: C 64 ILE cc_start: 0.8705 (mt) cc_final: 0.8355 (mt) REVERT: C 232 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7442 (tptm) REVERT: C 299 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8668 (mm-40) REVERT: C 400 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: C 403 ASN cc_start: 0.7442 (m-40) cc_final: 0.7215 (m-40) REVERT: C 459 LYS cc_start: 0.8529 (tttm) cc_final: 0.8200 (tttt) outliers start: 73 outliers final: 43 residues processed: 229 average time/residue: 0.5451 time to fit residues: 138.4149 Evaluate side-chains 229 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 86 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN G 39 GLN D 39 GLN E 39 GLN F 39 GLN H 6 GLN H 39 GLN I 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.154788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119059 restraints weight = 19156.071| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.42 r_work: 0.3167 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17358 Z= 0.227 Angle : 0.727 9.289 23649 Z= 0.375 Chirality : 0.051 0.445 2640 Planarity : 0.006 0.056 3003 Dihedral : 7.429 54.300 3008 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.86 % Favored : 97.00 % Rotamer: Outliers : 5.81 % Allowed : 21.05 % Favored : 73.14 % 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 aren not related in a simple way. whole: 0.31 (0.18), residues: 2100 helix: 2.44 (0.28), residues: 330 sheet: 1.25 (0.21), residues: 564 loop : -1.02 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 30 TYR 0.016 0.002 TYR I 99 PHE 0.020 0.002 PHE C 128 TRP 0.010 0.002 TRP B 93 HIS 0.006 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00542 (17307) covalent geometry : angle 0.70542 (23514) SS BOND : bond 0.00669 ( 18) SS BOND : angle 1.71033 ( 36) hydrogen bonds : bond 0.08026 ( 633) hydrogen bonds : angle 5.04845 ( 1809) link_BETA1-4 : bond 0.00787 ( 9) link_BETA1-4 : angle 2.54624 ( 27) link_NAG-ASN : bond 0.00796 ( 24) link_NAG-ASN : angle 2.69440 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 189 time to evaluate : 0.737 Fit side-chains REVERT: G 9 SER cc_start: 0.6803 (p) cc_final: 0.6518 (t) REVERT: G 19 THR cc_start: 0.5890 (OUTLIER) cc_final: 0.5578 (t) REVERT: D 74 ASP cc_start: 0.8603 (m-30) cc_final: 0.8383 (m-30) REVERT: F 63 LYS cc_start: 0.7723 (ttpt) cc_final: 0.7381 (ttmm) REVERT: A 162 ARG cc_start: 0.8860 (mpt180) cc_final: 0.8559 (mpt90) REVERT: A 232 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7483 (tptm) REVERT: A 381 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: A 400 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: A 403 ASN cc_start: 0.6875 (OUTLIER) cc_final: 0.6542 (m-40) REVERT: A 459 LYS cc_start: 0.8759 (tttm) cc_final: 0.8440 (tttt) REVERT: A 486 LYS cc_start: 0.6792 (mmpt) cc_final: 0.6455 (pptt) REVERT: B 162 ARG cc_start: 0.8869 (mpt180) cc_final: 0.8581 (mpt90) REVERT: B 232 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7541 (tptm) REVERT: B 381 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: B 400 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: B 403 ASN cc_start: 0.7463 (m-40) cc_final: 0.7198 (m-40) REVERT: B 459 LYS cc_start: 0.8673 (tttm) cc_final: 0.8340 (tttt) REVERT: B 486 LYS cc_start: 0.6881 (mmpt) cc_final: 0.6525 (pptt) REVERT: C 64 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8390 (mt) REVERT: C 232 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7492 (tptm) REVERT: C 381 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: C 400 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: C 403 ASN cc_start: 0.7551 (m-40) cc_final: 0.7314 (m-40) REVERT: C 459 LYS cc_start: 0.8674 (tttm) cc_final: 0.8351 (tttt) REVERT: C 486 LYS cc_start: 0.6791 (mmpt) cc_final: 0.6430 (pptt) REVERT: H 9 SER cc_start: 0.6752 (p) cc_final: 0.6548 (t) REVERT: H 19 THR cc_start: 0.5852 (OUTLIER) cc_final: 0.5557 (t) REVERT: I 9 SER cc_start: 0.6534 (p) cc_final: 0.6239 (t) REVERT: I 19 THR cc_start: 0.5780 (OUTLIER) cc_final: 0.5505 (t) outliers start: 98 outliers final: 55 residues processed: 260 average time/residue: 0.5273 time to fit residues: 153.7463 Evaluate side-chains 255 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 186 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 153 optimal weight: 6.9990 chunk 181 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120287 restraints weight = 19089.953| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.28 r_work: 0.3204 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17358 Z= 0.174 Angle : 0.648 8.736 23649 Z= 0.334 Chirality : 0.048 0.430 2640 Planarity : 0.005 0.053 3003 Dihedral : 7.123 57.925 3008 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.43 % Favored : 97.42 % Rotamer: Outliers : 5.36 % Allowed : 22.00 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.18), residues: 2100 helix: 2.55 (0.28), residues: 330 sheet: 1.14 (0.21), residues: 576 loop : -0.95 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 87 TYR 0.014 0.002 TYR I 99 PHE 0.019 0.002 PHE C 453 TRP 0.009 0.001 TRP A 435 HIS 0.006 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00403 (17307) covalent geometry : angle 0.62383 (23514) SS BOND : bond 0.00575 ( 18) SS BOND : angle 1.54441 ( 36) hydrogen bonds : bond 0.07141 ( 633) hydrogen bonds : angle 4.88257 ( 1809) link_BETA1-4 : bond 0.00555 ( 9) link_BETA1-4 : angle 2.36454 ( 27) link_NAG-ASN : bond 0.00507 ( 24) link_NAG-ASN : angle 2.75160 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 192 time to evaluate : 0.543 Fit side-chains REVERT: G 9 SER cc_start: 0.6759 (p) cc_final: 0.6478 (t) REVERT: G 19 THR cc_start: 0.5875 (OUTLIER) cc_final: 0.5580 (t) REVERT: G 52 ASN cc_start: 0.6496 (OUTLIER) cc_final: 0.6170 (t0) REVERT: D 74 ASP cc_start: 0.8610 (m-30) cc_final: 0.8387 (m-30) REVERT: A 68 GLN cc_start: 0.9004 (mt0) cc_final: 0.8564 (mt0) REVERT: A 162 ARG cc_start: 0.8836 (mpt180) cc_final: 0.8546 (mpt90) REVERT: A 232 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7476 (tptm) REVERT: A 400 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: A 459 LYS cc_start: 0.8697 (tttm) cc_final: 0.8369 (tttt) REVERT: A 486 LYS cc_start: 0.6824 (mmpt) cc_final: 0.6499 (pptt) REVERT: B 162 ARG cc_start: 0.8849 (mpt180) cc_final: 0.8572 (mpt90) REVERT: B 232 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7536 (tptm) REVERT: B 400 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: B 403 ASN cc_start: 0.7411 (m-40) cc_final: 0.7186 (m-40) REVERT: B 459 LYS cc_start: 0.8622 (tttm) cc_final: 0.8290 (tttt) REVERT: B 486 LYS cc_start: 0.6914 (mmpt) cc_final: 0.6581 (pptt) REVERT: C 64 ILE cc_start: 0.8682 (mt) cc_final: 0.8348 (mt) REVERT: C 232 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7480 (tptm) REVERT: C 400 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: C 403 ASN cc_start: 0.7509 (m-40) cc_final: 0.7292 (m-40) REVERT: C 459 LYS cc_start: 0.8603 (tttm) cc_final: 0.8269 (tttt) REVERT: C 486 LYS cc_start: 0.6816 (mmpt) cc_final: 0.6488 (pptt) REVERT: H 19 THR cc_start: 0.5869 (OUTLIER) cc_final: 0.5567 (t) REVERT: I 9 SER cc_start: 0.6509 (p) cc_final: 0.6233 (t) REVERT: I 19 THR cc_start: 0.5826 (OUTLIER) cc_final: 0.5571 (t) REVERT: I 52 ASN cc_start: 0.6341 (OUTLIER) cc_final: 0.6108 (t0) outliers start: 90 outliers final: 58 residues processed: 261 average time/residue: 0.5372 time to fit residues: 157.0226 Evaluate side-chains 256 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 187 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 170 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120549 restraints weight = 19044.811| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.36 r_work: 0.3200 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17358 Z= 0.166 Angle : 0.639 8.529 23649 Z= 0.330 Chirality : 0.048 0.430 2640 Planarity : 0.005 0.053 3003 Dihedral : 6.900 58.392 3008 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.38 % Favored : 97.47 % Rotamer: Outliers : 5.92 % Allowed : 21.78 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.18), residues: 2100 helix: 2.61 (0.28), residues: 330 sheet: 1.18 (0.21), residues: 576 loop : -0.94 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 87 TYR 0.014 0.002 TYR I 99 PHE 0.019 0.002 PHE C 128 TRP 0.009 0.001 TRP A 435 HIS 0.006 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00383 (17307) covalent geometry : angle 0.61583 (23514) SS BOND : bond 0.00493 ( 18) SS BOND : angle 1.52480 ( 36) hydrogen bonds : bond 0.07058 ( 633) hydrogen bonds : angle 4.84735 ( 1809) link_BETA1-4 : bond 0.00535 ( 9) link_BETA1-4 : angle 2.19335 ( 27) link_NAG-ASN : bond 0.00462 ( 24) link_NAG-ASN : angle 2.69590 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 192 time to evaluate : 0.420 Fit side-chains REVERT: G 9 SER cc_start: 0.6705 (p) cc_final: 0.6419 (t) REVERT: G 19 THR cc_start: 0.5914 (OUTLIER) cc_final: 0.5633 (t) REVERT: G 52 ASN cc_start: 0.6409 (OUTLIER) cc_final: 0.6003 (t0) REVERT: D 74 ASP cc_start: 0.8600 (m-30) cc_final: 0.8367 (m-30) REVERT: A 68 GLN cc_start: 0.9015 (mt0) cc_final: 0.8584 (mt0) REVERT: A 162 ARG cc_start: 0.8839 (mpt180) cc_final: 0.8557 (mpt90) REVERT: A 232 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7460 (tptm) REVERT: A 381 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: A 400 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: A 403 ASN cc_start: 0.6956 (OUTLIER) cc_final: 0.6633 (m-40) REVERT: A 459 LYS cc_start: 0.8688 (tttm) cc_final: 0.8361 (tttt) REVERT: A 486 LYS cc_start: 0.6820 (mmpt) cc_final: 0.6523 (pptt) REVERT: B 90 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8065 (tttm) REVERT: B 162 ARG cc_start: 0.8854 (mpt180) cc_final: 0.8581 (mpt90) REVERT: B 232 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7532 (tptm) REVERT: B 381 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: B 400 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: B 403 ASN cc_start: 0.7440 (m-40) cc_final: 0.7210 (m-40) REVERT: B 459 LYS cc_start: 0.8607 (tttm) cc_final: 0.8276 (tttt) REVERT: B 486 LYS cc_start: 0.6906 (mmpt) cc_final: 0.6595 (pptt) REVERT: C 64 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8344 (mt) REVERT: C 232 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7464 (tptm) REVERT: C 381 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: C 400 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: C 403 ASN cc_start: 0.7529 (m-40) cc_final: 0.7302 (m-40) REVERT: C 459 LYS cc_start: 0.8585 (tttm) cc_final: 0.8251 (tttt) REVERT: C 486 LYS cc_start: 0.6782 (mmpt) cc_final: 0.6486 (pptt) REVERT: H 19 THR cc_start: 0.5898 (OUTLIER) cc_final: 0.5592 (t) REVERT: I 9 SER cc_start: 0.6528 (p) cc_final: 0.6273 (t) REVERT: I 19 THR cc_start: 0.5875 (OUTLIER) cc_final: 0.5628 (t) REVERT: I 52 ASN cc_start: 0.6275 (OUTLIER) cc_final: 0.5937 (t0) outliers start: 100 outliers final: 65 residues processed: 265 average time/residue: 0.4926 time to fit residues: 146.2864 Evaluate side-chains 270 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 188 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 158 optimal weight: 0.0770 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN I 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120144 restraints weight = 19078.514| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.33 r_work: 0.3196 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17358 Z= 0.174 Angle : 0.649 9.018 23649 Z= 0.334 Chirality : 0.048 0.439 2640 Planarity : 0.005 0.052 3003 Dihedral : 6.818 56.073 3007 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.05 % Favored : 97.81 % Rotamer: Outliers : 5.81 % Allowed : 21.89 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.17), residues: 2100 helix: 2.61 (0.28), residues: 330 sheet: 1.19 (0.21), residues: 576 loop : -0.96 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 30 TYR 0.015 0.002 TYR I 99 PHE 0.019 0.002 PHE C 453 TRP 0.009 0.001 TRP A 435 HIS 0.006 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00406 (17307) covalent geometry : angle 0.62593 (23514) SS BOND : bond 0.00560 ( 18) SS BOND : angle 1.56247 ( 36) hydrogen bonds : bond 0.07179 ( 633) hydrogen bonds : angle 4.86446 ( 1809) link_BETA1-4 : bond 0.00537 ( 9) link_BETA1-4 : angle 2.18969 ( 27) link_NAG-ASN : bond 0.00458 ( 24) link_NAG-ASN : angle 2.71685 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 187 time to evaluate : 0.532 Fit side-chains REVERT: G 9 SER cc_start: 0.6701 (p) cc_final: 0.6402 (t) REVERT: G 19 THR cc_start: 0.5892 (OUTLIER) cc_final: 0.5613 (t) REVERT: D 74 ASP cc_start: 0.8609 (m-30) cc_final: 0.8383 (m-30) REVERT: A 68 GLN cc_start: 0.9018 (mt0) cc_final: 0.8586 (mt0) REVERT: A 162 ARG cc_start: 0.8839 (mpt180) cc_final: 0.8551 (mpt90) REVERT: A 232 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7456 (tptm) REVERT: A 381 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: A 400 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: A 403 ASN cc_start: 0.6974 (OUTLIER) cc_final: 0.6646 (m-40) REVERT: A 459 LYS cc_start: 0.8695 (tttm) cc_final: 0.8368 (tttt) REVERT: A 486 LYS cc_start: 0.6866 (mmpt) cc_final: 0.6539 (pptt) REVERT: B 90 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8063 (tttm) REVERT: B 162 ARG cc_start: 0.8854 (mpt180) cc_final: 0.8582 (mpt90) REVERT: B 232 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7525 (tptm) REVERT: B 381 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8119 (mt0) REVERT: B 400 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: B 403 ASN cc_start: 0.7436 (m-40) cc_final: 0.7218 (m-40) REVERT: B 459 LYS cc_start: 0.8616 (tttm) cc_final: 0.8287 (tttt) REVERT: B 486 LYS cc_start: 0.6960 (mmpt) cc_final: 0.6624 (pptt) REVERT: C 64 ILE cc_start: 0.8671 (mt) cc_final: 0.8329 (mt) REVERT: C 232 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7461 (tptm) REVERT: C 381 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: C 400 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: C 403 ASN cc_start: 0.7533 (m-40) cc_final: 0.7309 (m-40) REVERT: C 459 LYS cc_start: 0.8597 (tttm) cc_final: 0.8264 (tttt) REVERT: C 486 LYS cc_start: 0.6782 (mmpt) cc_final: 0.6488 (pptt) REVERT: H 19 THR cc_start: 0.5899 (OUTLIER) cc_final: 0.5598 (t) REVERT: I 9 SER cc_start: 0.6575 (p) cc_final: 0.6303 (t) REVERT: I 19 THR cc_start: 0.5859 (OUTLIER) cc_final: 0.5610 (t) outliers start: 98 outliers final: 69 residues processed: 261 average time/residue: 0.5431 time to fit residues: 159.1612 Evaluate side-chains 269 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 186 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 134 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 52 ASN H 6 GLN I 6 GLN I 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120080 restraints weight = 19177.214| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.29 r_work: 0.3204 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17358 Z= 0.173 Angle : 0.651 9.083 23649 Z= 0.336 Chirality : 0.048 0.441 2640 Planarity : 0.005 0.053 3003 Dihedral : 6.599 47.815 3003 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.19 % Favored : 97.66 % Rotamer: Outliers : 5.70 % Allowed : 22.17 % Favored : 72.14 % 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 aren not related in a simple way. whole: 0.44 (0.18), residues: 2100 helix: 2.67 (0.28), residues: 324 sheet: 1.25 (0.21), residues: 603 loop : -0.98 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 30 TYR 0.015 0.002 TYR I 99 PHE 0.018 0.002 PHE A 128 TRP 0.009 0.001 TRP A 435 HIS 0.006 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00402 (17307) covalent geometry : angle 0.62833 (23514) SS BOND : bond 0.00533 ( 18) SS BOND : angle 1.51742 ( 36) hydrogen bonds : bond 0.07154 ( 633) hydrogen bonds : angle 4.85303 ( 1809) link_BETA1-4 : bond 0.00550 ( 9) link_BETA1-4 : angle 2.12846 ( 27) link_NAG-ASN : bond 0.00470 ( 24) link_NAG-ASN : angle 2.71994 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 187 time to evaluate : 0.622 Fit side-chains REVERT: G 9 SER cc_start: 0.6685 (p) cc_final: 0.6392 (t) REVERT: G 19 THR cc_start: 0.5922 (OUTLIER) cc_final: 0.5648 (t) REVERT: D 74 ASP cc_start: 0.8615 (m-30) cc_final: 0.8390 (m-30) REVERT: A 68 GLN cc_start: 0.9009 (mt0) cc_final: 0.8578 (mt0) REVERT: A 162 ARG cc_start: 0.8832 (mpt180) cc_final: 0.8546 (mpt90) REVERT: A 232 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7469 (tptm) REVERT: A 259 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8288 (mt-10) REVERT: A 381 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: A 400 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: A 403 ASN cc_start: 0.6983 (OUTLIER) cc_final: 0.6606 (m-40) REVERT: A 459 LYS cc_start: 0.8686 (tttm) cc_final: 0.8359 (tttt) REVERT: A 486 LYS cc_start: 0.6887 (mmpt) cc_final: 0.6564 (pptt) REVERT: B 90 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8064 (tttm) REVERT: B 162 ARG cc_start: 0.8841 (mpt180) cc_final: 0.8571 (mpt90) REVERT: B 232 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7530 (tptm) REVERT: B 381 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: B 400 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: B 403 ASN cc_start: 0.7427 (m-40) cc_final: 0.7190 (m-40) REVERT: B 459 LYS cc_start: 0.8614 (tttm) cc_final: 0.8286 (tttt) REVERT: B 486 LYS cc_start: 0.6950 (mmpt) cc_final: 0.6617 (pptt) REVERT: C 64 ILE cc_start: 0.8671 (mt) cc_final: 0.8330 (mt) REVERT: C 232 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7469 (tptm) REVERT: C 370 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7335 (tp-100) REVERT: C 381 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8012 (mt0) REVERT: C 400 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: C 403 ASN cc_start: 0.7523 (m-40) cc_final: 0.7302 (m-40) REVERT: C 459 LYS cc_start: 0.8599 (tttm) cc_final: 0.8266 (tttt) REVERT: C 486 LYS cc_start: 0.6823 (mmpt) cc_final: 0.6538 (pptt) REVERT: H 19 THR cc_start: 0.5899 (OUTLIER) cc_final: 0.5601 (t) REVERT: I 9 SER cc_start: 0.6534 (p) cc_final: 0.6256 (t) REVERT: I 19 THR cc_start: 0.5904 (OUTLIER) cc_final: 0.5665 (t) outliers start: 96 outliers final: 70 residues processed: 261 average time/residue: 0.5335 time to fit residues: 155.4633 Evaluate side-chains 270 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 184 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 9 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120473 restraints weight = 19048.474| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.13 r_work: 0.3210 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17358 Z= 0.181 Angle : 0.660 9.455 23649 Z= 0.340 Chirality : 0.049 0.449 2640 Planarity : 0.005 0.052 3003 Dihedral : 6.620 48.167 3003 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.15 % Favored : 97.71 % Rotamer: Outliers : 5.64 % Allowed : 22.17 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.18), residues: 2100 helix: 2.66 (0.28), residues: 324 sheet: 1.25 (0.20), residues: 603 loop : -0.99 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 30 TYR 0.016 0.002 TYR I 99 PHE 0.019 0.002 PHE C 453 TRP 0.009 0.002 TRP A 435 HIS 0.006 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00423 (17307) covalent geometry : angle 0.63687 (23514) SS BOND : bond 0.00578 ( 18) SS BOND : angle 1.56620 ( 36) hydrogen bonds : bond 0.07290 ( 633) hydrogen bonds : angle 4.87764 ( 1809) link_BETA1-4 : bond 0.00518 ( 9) link_BETA1-4 : angle 2.13637 ( 27) link_NAG-ASN : bond 0.00471 ( 24) link_NAG-ASN : angle 2.76749 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 188 time to evaluate : 0.644 Fit side-chains REVERT: G 9 SER cc_start: 0.6688 (p) cc_final: 0.6399 (t) REVERT: G 19 THR cc_start: 0.5927 (OUTLIER) cc_final: 0.5651 (t) REVERT: D 74 ASP cc_start: 0.8608 (m-30) cc_final: 0.8383 (m-30) REVERT: A 68 GLN cc_start: 0.8999 (mt0) cc_final: 0.8569 (mt0) REVERT: A 162 ARG cc_start: 0.8813 (mpt180) cc_final: 0.8528 (mpt90) REVERT: A 232 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7493 (tptm) REVERT: A 259 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8265 (mt-10) REVERT: A 381 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: A 400 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: A 403 ASN cc_start: 0.6990 (OUTLIER) cc_final: 0.6599 (m-40) REVERT: A 459 LYS cc_start: 0.8695 (tttm) cc_final: 0.8389 (tttt) REVERT: A 486 LYS cc_start: 0.6881 (mmpt) cc_final: 0.6553 (pptt) REVERT: B 90 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8073 (tttm) REVERT: B 162 ARG cc_start: 0.8834 (mpt180) cc_final: 0.8565 (mpt90) REVERT: B 232 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7541 (tptm) REVERT: B 381 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: B 400 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: B 403 ASN cc_start: 0.7424 (m-40) cc_final: 0.7190 (m-40) REVERT: B 459 LYS cc_start: 0.8625 (tttm) cc_final: 0.8308 (tttt) REVERT: B 486 LYS cc_start: 0.6958 (mmpt) cc_final: 0.6643 (pptt) REVERT: C 64 ILE cc_start: 0.8668 (mt) cc_final: 0.8343 (mt) REVERT: C 232 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7483 (tptm) REVERT: C 370 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7350 (tp-100) REVERT: C 381 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8019 (mt0) REVERT: C 400 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: C 403 ASN cc_start: 0.7509 (m-40) cc_final: 0.7291 (m-40) REVERT: C 459 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8286 (tttt) REVERT: C 486 LYS cc_start: 0.6830 (mmpt) cc_final: 0.6567 (pptt) REVERT: H 19 THR cc_start: 0.5913 (OUTLIER) cc_final: 0.5617 (t) REVERT: I 9 SER cc_start: 0.6554 (p) cc_final: 0.6273 (t) REVERT: I 19 THR cc_start: 0.5916 (OUTLIER) cc_final: 0.5680 (t) outliers start: 95 outliers final: 71 residues processed: 258 average time/residue: 0.5689 time to fit residues: 163.9848 Evaluate side-chains 273 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 185 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 182 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121123 restraints weight = 18993.313| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.08 r_work: 0.3222 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17358 Z= 0.158 Angle : 0.629 9.284 23649 Z= 0.325 Chirality : 0.047 0.431 2640 Planarity : 0.005 0.052 3003 Dihedral : 6.508 47.790 3003 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.10 % Favored : 97.76 % Rotamer: Outliers : 4.97 % Allowed : 22.95 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.18), residues: 2100 helix: 2.75 (0.28), residues: 324 sheet: 1.29 (0.21), residues: 603 loop : -0.96 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 30 TYR 0.015 0.002 TYR I 99 PHE 0.018 0.002 PHE C 128 TRP 0.009 0.001 TRP A 435 HIS 0.005 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00362 (17307) covalent geometry : angle 0.60689 (23514) SS BOND : bond 0.00526 ( 18) SS BOND : angle 1.51608 ( 36) hydrogen bonds : bond 0.06903 ( 633) hydrogen bonds : angle 4.79657 ( 1809) link_BETA1-4 : bond 0.00530 ( 9) link_BETA1-4 : angle 2.02514 ( 27) link_NAG-ASN : bond 0.00464 ( 24) link_NAG-ASN : angle 2.67633 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4200 Ramachandran restraints generated. 2100 Oldfield, 0 Emsley, 2100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 189 time to evaluate : 0.720 Fit side-chains REVERT: G 9 SER cc_start: 0.6749 (p) cc_final: 0.6472 (t) REVERT: G 19 THR cc_start: 0.5913 (OUTLIER) cc_final: 0.5641 (t) REVERT: D 74 ASP cc_start: 0.8569 (m-30) cc_final: 0.8344 (m-30) REVERT: A 68 GLN cc_start: 0.9000 (mt0) cc_final: 0.8566 (mt0) REVERT: A 162 ARG cc_start: 0.8817 (mpt180) cc_final: 0.8533 (mpt90) REVERT: A 232 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7470 (tptm) REVERT: A 259 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: A 381 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: A 400 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: A 403 ASN cc_start: 0.6959 (OUTLIER) cc_final: 0.6584 (m-40) REVERT: A 459 LYS cc_start: 0.8669 (tttm) cc_final: 0.8360 (tttt) REVERT: A 486 LYS cc_start: 0.6856 (mmpt) cc_final: 0.6559 (pptt) REVERT: B 90 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8051 (tttm) REVERT: B 162 ARG cc_start: 0.8836 (mpt180) cc_final: 0.8571 (mpt90) REVERT: B 232 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7538 (tptm) REVERT: B 381 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: B 400 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: B 403 ASN cc_start: 0.7409 (m-40) cc_final: 0.7185 (m-40) REVERT: B 459 LYS cc_start: 0.8595 (tttm) cc_final: 0.8272 (tttt) REVERT: B 486 LYS cc_start: 0.6945 (mmpt) cc_final: 0.6639 (pptt) REVERT: C 64 ILE cc_start: 0.8670 (mt) cc_final: 0.8311 (mt) REVERT: C 232 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7478 (tptm) REVERT: C 370 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7374 (tp-100) REVERT: C 381 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: C 400 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: C 403 ASN cc_start: 0.7501 (m-40) cc_final: 0.7278 (m-40) REVERT: C 459 LYS cc_start: 0.8573 (tttm) cc_final: 0.8242 (tttt) REVERT: C 486 LYS cc_start: 0.6833 (mmpt) cc_final: 0.6577 (pptt) REVERT: H 19 THR cc_start: 0.5896 (OUTLIER) cc_final: 0.5604 (t) REVERT: I 9 SER cc_start: 0.6617 (p) cc_final: 0.6273 (t) outliers start: 83 outliers final: 63 residues processed: 250 average time/residue: 0.6303 time to fit residues: 176.2155 Evaluate side-chains 267 residues out of total 1806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 189 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 40 optimal weight: 0.0980 chunk 85 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.156650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121016 restraints weight = 19029.581| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.26 r_work: 0.3217 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17358 Z= 0.151 Angle : 0.615 9.262 23649 Z= 0.317 Chirality : 0.047 0.420 2640 Planarity : 0.005 0.052 3003 Dihedral : 6.434 47.870 3003 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.05 % Favored : 97.81 % Rotamer: Outliers : 4.86 % Allowed : 22.95 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.18), residues: 2100 helix: 2.83 (0.28), residues: 324 sheet: 1.31 (0.21), residues: 603 loop : -0.94 (0.16), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 87 TYR 0.015 0.002 TYR I 99 PHE 0.018 0.002 PHE C 128 TRP 0.009 0.001 TRP A 435 HIS 0.005 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00341 (17307) covalent geometry : angle 0.59243 (23514) SS BOND : bond 0.00504 ( 18) SS BOND : angle 1.48800 ( 36) hydrogen bonds : bond 0.06791 ( 633) hydrogen bonds : angle 4.75950 ( 1809) link_BETA1-4 : bond 0.00526 ( 9) link_BETA1-4 : angle 1.96682 ( 27) link_NAG-ASN : bond 0.00456 ( 24) link_NAG-ASN : angle 2.61854 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6995.15 seconds wall clock time: 119 minutes 31.05 seconds (7171.05 seconds total)