Starting phenix.real_space_refine on Thu Sep 18 15:27:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dn2_47024/09_2025/9dn2_47024.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dn2_47024/09_2025/9dn2_47024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dn2_47024/09_2025/9dn2_47024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dn2_47024/09_2025/9dn2_47024.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dn2_47024/09_2025/9dn2_47024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dn2_47024/09_2025/9dn2_47024.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 10848 2.51 5 N 2973 2.21 5 O 3498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17397 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3950 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 480} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "I" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "J" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 791 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "M" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 791 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "N" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 791 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "B" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3950 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 480} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3950 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 480} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.42, per 1000 atoms: 0.25 Number of scatterers: 17397 At special positions: 0 Unit cell: (145.369, 138.811, 149.741, 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 78 16.00 O 3498 8.00 N 2973 7.00 C 10848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 601 " - " ASN A 8 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 158 " " NAG A 604 " - " ASN A 126 " " NAG A 605 " - " ASN A 483 " " NAG B 601 " - " ASN B 8 " " NAG B 602 " - " ASN B 133 " " NAG B 603 " - " ASN B 158 " " NAG B 604 " - " ASN B 126 " " NAG B 605 " - " ASN B 483 " " NAG C 601 " - " ASN C 8 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 158 " " NAG C 604 " - " ASN C 126 " " NAG C 605 " - " ASN C 483 " " NAG D 1 " - " ASN A 285 " " NAG E 1 " - " ASN A 246 " " NAG F 1 " - " ASN A 38 " " NAG G 1 " - " ASN A 165 " " NAG K 1 " - " ASN A 63 " " NAG O 1 " - " ASN B 285 " " NAG P 1 " - " ASN B 246 " " NAG Q 1 " - " ASN B 38 " " NAG R 1 " - " ASN B 165 " " NAG S 1 " - " ASN B 63 " " NAG T 1 " - " ASN C 285 " " NAG U 1 " - " ASN C 246 " " NAG V 1 " - " ASN C 38 " " NAG W 1 " - " ASN C 165 " " NAG X 1 " - " ASN C 63 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 819.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 45 sheets defined 19.4% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.718A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.683A pdb=" N SER A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.720A pdb=" N LEU A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 4.020A pdb=" N LEU A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 446 removed outlier: 4.444A pdb=" N MET A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.711A pdb=" N GLY A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.872A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 4.084A pdb=" N PHE H 37 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.668A pdb=" N THR H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 37 removed outlier: 4.082A pdb=" N PHE I 37 " --> pdb=" O PHE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 99 removed outlier: 3.669A pdb=" N THR I 99 " --> pdb=" O SER I 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 37 removed outlier: 4.082A pdb=" N PHE J 37 " --> pdb=" O PHE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.669A pdb=" N THR J 99 " --> pdb=" O SER J 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 5.717A pdb=" N GLY B 78 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.683A pdb=" N SER B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.720A pdb=" N LEU B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 385 removed outlier: 4.020A pdb=" N LEU B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 446 removed outlier: 4.444A pdb=" N MET B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 474 through 484 removed outlier: 3.711A pdb=" N GLY B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.871A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 5.717A pdb=" N GLY C 78 " --> pdb=" O GLN C 75 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.682A pdb=" N SER C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.719A pdb=" N LEU C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 385 removed outlier: 4.020A pdb=" N LEU C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 446 removed outlier: 4.443A pdb=" N MET C 444 " --> pdb=" O THR C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 474 through 484 removed outlier: 3.711A pdb=" N GLY C 479 " --> pdb=" O ASN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.871A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN C 497 " --> pdb=" O ASP C 493 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 3.685A pdb=" N HIS A 355 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 removed outlier: 3.813A pdb=" N ARG A 90 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101 removed outlier: 3.705A pdb=" N ILE A 232 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 140 removed outlier: 4.766A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.321A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 288 " --> pdb=" O CYS A 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 461 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.512A pdb=" N SER H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.746A pdb=" N TRP H 41 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TRP H 55 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU H 39 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS H 106 " --> pdb=" O GLY H 116 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY H 116 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.513A pdb=" N SER I 22 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 65 through 67 removed outlier: 6.747A pdb=" N TRP I 41 " --> pdb=" O MET I 53 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP I 55 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU I 39 " --> pdb=" O TRP I 55 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS I 106 " --> pdb=" O GLY I 116 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY I 116 " --> pdb=" O LYS I 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.512A pdb=" N SER J 22 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 65 through 67 removed outlier: 6.746A pdb=" N TRP J 41 " --> pdb=" O MET J 53 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP J 55 " --> pdb=" O LEU J 39 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU J 39 " --> pdb=" O TRP J 55 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS J 106 " --> pdb=" O GLY J 116 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY J 116 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.825A pdb=" N ALA L 87 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 49 through 53 removed outlier: 3.661A pdb=" N ALA L 49 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU L 45 " --> pdb=" O ALA L 49 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 19 through 23 removed outlier: 3.827A pdb=" N ALA M 87 " --> pdb=" O CYS M 23 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 49 through 53 removed outlier: 3.660A pdb=" N ALA M 49 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU M 45 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 19 through 23 removed outlier: 3.826A pdb=" N ALA N 87 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 49 through 53 removed outlier: 3.660A pdb=" N ALA N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU N 45 " --> pdb=" O ALA N 49 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 14 through 17 removed outlier: 3.687A pdb=" N HIS B 355 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AC9, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'B' and resid 58 through 61 removed outlier: 3.813A pdb=" N ARG B 90 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 100 through 101 removed outlier: 3.706A pdb=" N ILE B 232 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AD4, first strand: chain 'B' and resid 136 through 140 removed outlier: 4.767A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'B' and resid 281 through 283 removed outlier: 4.321A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 288 " --> pdb=" O CYS B 281 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AD8, first strand: chain 'C' and resid 14 through 17 removed outlier: 3.686A pdb=" N HIS C 355 " --> pdb=" O GLY C 362 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AE1, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AE2, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'C' and resid 58 through 61 removed outlier: 3.813A pdb=" N ARG C 90 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 100 through 101 removed outlier: 3.706A pdb=" N ILE C 232 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AE6, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.766A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AE8, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.322A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C 288 " --> pdb=" O CYS C 281 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 459 through 461 576 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5626 1.34 - 1.46: 4117 1.46 - 1.58: 7912 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 17763 Sorted by residual: bond pdb=" C SER C 54 " pdb=" N PRO C 55 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.18e-01 bond pdb=" C SER B 54 " pdb=" N PRO B 55 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.84e-01 bond pdb=" C SER A 54 " pdb=" N PRO A 55 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.55e-01 bond pdb=" N GLY M 70 " pdb=" CA GLY M 70 " ideal model delta sigma weight residual 1.449 1.437 0.013 1.45e-02 4.76e+03 7.45e-01 bond pdb=" C2 NAG B 605 " pdb=" N2 NAG B 605 " ideal model delta sigma weight residual 1.439 1.456 -0.017 2.00e-02 2.50e+03 7.33e-01 ... (remaining 17758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 23618 1.84 - 3.69: 416 3.69 - 5.53: 36 5.53 - 7.37: 8 7.37 - 9.22: 6 Bond angle restraints: 24084 Sorted by residual: angle pdb=" C GLN N 44 " pdb=" N LEU N 45 " pdb=" CA LEU N 45 " ideal model delta sigma weight residual 122.31 130.07 -7.76 2.34e+00 1.83e-01 1.10e+01 angle pdb=" C GLN L 44 " pdb=" N LEU L 45 " pdb=" CA LEU L 45 " ideal model delta sigma weight residual 122.31 130.01 -7.70 2.34e+00 1.83e-01 1.08e+01 angle pdb=" C GLN M 44 " pdb=" N LEU M 45 " pdb=" CA LEU M 45 " ideal model delta sigma weight residual 122.31 130.00 -7.69 2.34e+00 1.83e-01 1.08e+01 angle pdb=" C2 NAG A 605 " pdb=" N2 NAG A 605 " pdb=" C7 NAG A 605 " ideal model delta sigma weight residual 124.56 133.78 -9.22 3.00e+00 1.11e-01 9.44e+00 angle pdb=" C2 NAG C 605 " pdb=" N2 NAG C 605 " pdb=" C7 NAG C 605 " ideal model delta sigma weight residual 124.56 133.75 -9.19 3.00e+00 1.11e-01 9.38e+00 ... (remaining 24079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 10401 17.33 - 34.65: 612 34.65 - 51.98: 141 51.98 - 69.30: 69 69.30 - 86.63: 24 Dihedral angle restraints: 11247 sinusoidal: 5094 harmonic: 6153 Sorted by residual: dihedral pdb=" CA GLN L 44 " pdb=" C GLN L 44 " pdb=" N LEU L 45 " pdb=" CA LEU L 45 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLN N 44 " pdb=" C GLN N 44 " pdb=" N LEU N 45 " pdb=" CA LEU N 45 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLN M 44 " pdb=" C GLN M 44 " pdb=" N LEU M 45 " pdb=" CA LEU M 45 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 11244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2198 0.049 - 0.099: 434 0.099 - 0.148: 103 0.148 - 0.197: 7 0.197 - 0.247: 9 Chirality restraints: 2751 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN B 246 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 246 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2748 not shown) Planarity restraints: 3114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 283 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 284 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 283 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO C 284 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 284 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 284 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 283 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO B 284 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " -0.030 5.00e-02 4.00e+02 ... (remaining 3111 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 9309 3.01 - 3.48: 16148 3.48 - 3.95: 26354 3.95 - 4.43: 29273 4.43 - 4.90: 51251 Nonbonded interactions: 132335 Sorted by model distance: nonbonded pdb=" C4 NAG W 2 " pdb=" O5 BMA W 3 " model vdw 2.531 2.776 nonbonded pdb=" C4 NAG R 2 " pdb=" O5 BMA R 3 " model vdw 2.531 2.776 nonbonded pdb=" C4 NAG G 2 " pdb=" O5 BMA G 3 " model vdw 2.531 2.776 nonbonded pdb=" O2 BMA G 3 " pdb=" O3 BMA G 3 " model vdw 2.559 2.432 nonbonded pdb=" C4 NAG K 1 " pdb=" O5 NAG K 2 " model vdw 2.559 2.776 ... (remaining 132330 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'W' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.670 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 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 : 0.002 0.029 17835 Z= 0.113 Angle : 0.614 9.217 24276 Z= 0.314 Chirality : 0.045 0.247 2751 Planarity : 0.004 0.054 3084 Dihedral : 13.015 86.629 7251 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.96 % Allowed : 7.35 % Favored : 90.69 % 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: -1.02 (0.18), residues: 2130 helix: 1.19 (0.28), residues: 342 sheet: -0.56 (0.20), residues: 606 loop : -1.32 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 109 TYR 0.008 0.001 TYR L 55 PHE 0.012 0.001 PHE A 174 TRP 0.011 0.001 TRP H 55 HIS 0.003 0.001 HIS C 471 Details of bonding type rmsd covalent geometry : bond 0.00223 (17763) covalent geometry : angle 0.59474 (24084) SS BOND : bond 0.00371 ( 24) SS BOND : angle 0.73850 ( 48) hydrogen bonds : bond 0.15896 ( 576) hydrogen bonds : angle 7.15125 ( 1512) link_BETA1-4 : bond 0.00580 ( 18) link_BETA1-4 : angle 2.45598 ( 54) link_NAG-ASN : bond 0.00369 ( 30) link_NAG-ASN : angle 1.76567 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 145 SER cc_start: 0.7626 (m) cc_final: 0.6972 (p) REVERT: A 264 LYS cc_start: 0.7351 (mttt) cc_final: 0.7016 (pttt) REVERT: A 329 ARG cc_start: 0.7472 (tmm-80) cc_final: 0.5940 (tpp-160) REVERT: A 447 LEU cc_start: 0.7318 (tp) cc_final: 0.6982 (tt) REVERT: A 455 LEU cc_start: 0.8744 (mt) cc_final: 0.8506 (mt) REVERT: A 462 MET cc_start: 0.7723 (mmm) cc_final: 0.7500 (mmm) REVERT: H 35 THR cc_start: 0.7861 (p) cc_final: 0.7583 (t) REVERT: I 67 PHE cc_start: 0.7586 (m-10) cc_final: 0.7263 (m-10) REVERT: J 35 THR cc_start: 0.8100 (p) cc_final: 0.7843 (t) REVERT: J 67 PHE cc_start: 0.7488 (m-10) cc_final: 0.7239 (m-10) REVERT: J 88 TYR cc_start: 0.7122 (m-80) cc_final: 0.6658 (m-80) REVERT: B 145 SER cc_start: 0.7531 (m) cc_final: 0.7009 (p) REVERT: B 264 LYS cc_start: 0.7295 (mttt) cc_final: 0.7021 (ptmt) REVERT: B 329 ARG cc_start: 0.7479 (tmm-80) cc_final: 0.5978 (tpp-160) REVERT: B 441 ASP cc_start: 0.7251 (t0) cc_final: 0.6930 (t0) REVERT: B 446 LYS cc_start: 0.7119 (ttmm) cc_final: 0.6902 (mtmt) REVERT: B 447 LEU cc_start: 0.7266 (tp) cc_final: 0.7045 (tt) REVERT: B 455 LEU cc_start: 0.8782 (mt) cc_final: 0.8536 (mt) REVERT: B 462 MET cc_start: 0.7835 (mmm) cc_final: 0.7381 (mmm) REVERT: C 33 ARG cc_start: 0.7845 (mmm160) cc_final: 0.7451 (mmp-170) REVERT: C 104 ASP cc_start: 0.7929 (t0) cc_final: 0.7662 (t70) REVERT: C 168 MET cc_start: 0.7867 (tpt) cc_final: 0.7629 (tpt) REVERT: C 264 LYS cc_start: 0.7464 (mttt) cc_final: 0.6964 (ptmt) REVERT: C 329 ARG cc_start: 0.7329 (tmm-80) cc_final: 0.5781 (tpp-160) REVERT: C 441 ASP cc_start: 0.7448 (t0) cc_final: 0.6809 (t0) outliers start: 36 outliers final: 18 residues processed: 324 average time/residue: 0.1072 time to fit residues: 54.6430 Evaluate side-chains 240 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 104 CYS Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0050 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 overall best weight: 0.4912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 357 ASN A 376 GLN N 66 ASN B 75 GLN B 295 GLN B 357 ASN B 376 GLN C 75 GLN C 295 GLN C 357 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.184364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.149299 restraints weight = 21159.849| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.18 r_work: 0.3628 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17835 Z= 0.117 Angle : 0.617 9.840 24276 Z= 0.305 Chirality : 0.046 0.249 2751 Planarity : 0.004 0.049 3084 Dihedral : 8.779 58.268 3352 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.89 % Allowed : 10.02 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.78 (0.18), residues: 2130 helix: 1.48 (0.28), residues: 348 sheet: -0.26 (0.21), residues: 585 loop : -1.28 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 456 TYR 0.010 0.001 TYR H 103 PHE 0.013 0.001 PHE B 353 TRP 0.009 0.001 TRP J 55 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00264 (17763) covalent geometry : angle 0.59520 (24084) SS BOND : bond 0.00342 ( 24) SS BOND : angle 1.66766 ( 48) hydrogen bonds : bond 0.03447 ( 576) hydrogen bonds : angle 5.49827 ( 1512) link_BETA1-4 : bond 0.00661 ( 18) link_BETA1-4 : angle 2.24011 ( 54) link_NAG-ASN : bond 0.00567 ( 30) link_NAG-ASN : angle 1.79599 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 0.697 Fit side-chains REVERT: A 197 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7302 (mm-40) REVERT: A 264 LYS cc_start: 0.7460 (mttt) cc_final: 0.6751 (pttt) REVERT: A 329 ARG cc_start: 0.7358 (tmm-80) cc_final: 0.5804 (tpp-160) REVERT: A 455 LEU cc_start: 0.8802 (mt) cc_final: 0.8531 (mt) REVERT: A 462 MET cc_start: 0.7782 (mmm) cc_final: 0.7501 (mmm) REVERT: H 78 MET cc_start: 0.6471 (pmm) cc_final: 0.6115 (pmm) REVERT: B 145 SER cc_start: 0.7616 (m) cc_final: 0.7052 (p) REVERT: B 197 GLN cc_start: 0.7339 (mm-40) cc_final: 0.7096 (mm-40) REVERT: B 259 LYS cc_start: 0.8145 (mttt) cc_final: 0.7639 (mtpp) REVERT: B 264 LYS cc_start: 0.7324 (mttt) cc_final: 0.6700 (ptmt) REVERT: B 329 ARG cc_start: 0.7323 (tmm-80) cc_final: 0.5792 (tpp-160) REVERT: B 375 ASP cc_start: 0.7617 (m-30) cc_final: 0.7279 (m-30) REVERT: B 444 MET cc_start: 0.6996 (mmm) cc_final: 0.5185 (tmm) REVERT: B 446 LYS cc_start: 0.6986 (ttmm) cc_final: 0.6776 (mtmt) REVERT: B 447 LEU cc_start: 0.7262 (tp) cc_final: 0.6944 (tt) REVERT: B 455 LEU cc_start: 0.8847 (mt) cc_final: 0.8589 (mt) REVERT: B 462 MET cc_start: 0.7755 (mmm) cc_final: 0.7490 (mmm) REVERT: C 33 ARG cc_start: 0.7882 (mmm160) cc_final: 0.7330 (mmp-170) REVERT: C 104 ASP cc_start: 0.7437 (t0) cc_final: 0.7196 (t70) REVERT: C 264 LYS cc_start: 0.7454 (mttt) cc_final: 0.6586 (ptmt) REVERT: C 329 ARG cc_start: 0.7213 (tmm-80) cc_final: 0.5572 (tpp-160) REVERT: C 467 PHE cc_start: 0.8072 (m-80) cc_final: 0.7796 (m-10) outliers start: 53 outliers final: 32 residues processed: 266 average time/residue: 0.1272 time to fit residues: 53.9018 Evaluate side-chains 254 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 17 optimal weight: 0.0170 chunk 143 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 116 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 75 GLN C 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.183854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149073 restraints weight = 21369.309| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.16 r_work: 0.3623 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17835 Z= 0.113 Angle : 0.592 9.786 24276 Z= 0.293 Chirality : 0.046 0.247 2751 Planarity : 0.004 0.051 3084 Dihedral : 8.459 58.103 3345 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.65 % Allowed : 10.57 % Favored : 85.78 % 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: -0.68 (0.18), residues: 2130 helix: 1.69 (0.28), residues: 348 sheet: -0.19 (0.21), residues: 585 loop : -1.26 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 33 TYR 0.011 0.001 TYR H 103 PHE 0.015 0.001 PHE C 120 TRP 0.011 0.001 TRP I 55 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00253 (17763) covalent geometry : angle 0.57380 (24084) SS BOND : bond 0.00332 ( 24) SS BOND : angle 1.06064 ( 48) hydrogen bonds : bond 0.03240 ( 576) hydrogen bonds : angle 5.21292 ( 1512) link_BETA1-4 : bond 0.00632 ( 18) link_BETA1-4 : angle 2.18726 ( 54) link_NAG-ASN : bond 0.00458 ( 30) link_NAG-ASN : angle 1.74719 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 227 time to evaluate : 0.714 Fit side-chains REVERT: A 145 SER cc_start: 0.7503 (m) cc_final: 0.6941 (p) REVERT: A 197 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7317 (mm-40) REVERT: A 264 LYS cc_start: 0.7459 (mttt) cc_final: 0.6739 (pttt) REVERT: A 329 ARG cc_start: 0.7291 (tmm-80) cc_final: 0.5836 (tpp-160) REVERT: A 455 LEU cc_start: 0.8835 (mt) cc_final: 0.8561 (mt) REVERT: A 462 MET cc_start: 0.7802 (mmm) cc_final: 0.7468 (mmm) REVERT: H 66 ASP cc_start: 0.7325 (t70) cc_final: 0.6904 (t70) REVERT: J 88 TYR cc_start: 0.6795 (m-80) cc_final: 0.6252 (m-80) REVERT: B 197 GLN cc_start: 0.7434 (mm-40) cc_final: 0.7224 (mm-40) REVERT: B 259 LYS cc_start: 0.8119 (mttt) cc_final: 0.7628 (mtpp) REVERT: B 268 MET cc_start: 0.7115 (ttp) cc_final: 0.6889 (ttm) REVERT: B 329 ARG cc_start: 0.7334 (tmm-80) cc_final: 0.5822 (tpp-160) REVERT: B 375 ASP cc_start: 0.7571 (m-30) cc_final: 0.7211 (m-30) REVERT: B 446 LYS cc_start: 0.7007 (ttmm) cc_final: 0.6794 (mtmt) REVERT: B 455 LEU cc_start: 0.8904 (mt) cc_final: 0.8629 (mt) REVERT: B 462 MET cc_start: 0.7788 (mmm) cc_final: 0.7520 (mmm) REVERT: C 33 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7329 (mmp-170) REVERT: C 104 ASP cc_start: 0.7462 (t0) cc_final: 0.7246 (t0) REVERT: C 264 LYS cc_start: 0.7437 (mttt) cc_final: 0.6595 (ptmt) REVERT: C 329 ARG cc_start: 0.7379 (tmm-80) cc_final: 0.5753 (tpp-160) outliers start: 67 outliers final: 44 residues processed: 272 average time/residue: 0.1258 time to fit residues: 54.5785 Evaluate side-chains 253 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 189 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 157 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140474 restraints weight = 21486.120| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.10 r_work: 0.3531 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17835 Z= 0.258 Angle : 0.732 9.688 24276 Z= 0.368 Chirality : 0.051 0.347 2751 Planarity : 0.005 0.052 3084 Dihedral : 8.860 59.455 3344 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.03 % Allowed : 12.15 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.25 (0.17), residues: 2130 helix: 0.97 (0.27), residues: 357 sheet: -0.47 (0.21), residues: 579 loop : -1.63 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 255 TYR 0.023 0.002 TYR H 103 PHE 0.015 0.002 PHE B 353 TRP 0.013 0.002 TRP C 84 HIS 0.011 0.003 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00621 (17763) covalent geometry : angle 0.71092 (24084) SS BOND : bond 0.00540 ( 24) SS BOND : angle 1.73154 ( 48) hydrogen bonds : bond 0.04142 ( 576) hydrogen bonds : angle 5.40785 ( 1512) link_BETA1-4 : bond 0.00725 ( 18) link_BETA1-4 : angle 2.45251 ( 54) link_NAG-ASN : bond 0.00511 ( 30) link_NAG-ASN : angle 2.04846 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 208 time to evaluate : 0.742 Fit side-chains REVERT: A 168 MET cc_start: 0.7943 (tpt) cc_final: 0.7581 (tpt) REVERT: A 210 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7124 (pm20) REVERT: A 264 LYS cc_start: 0.7481 (mttt) cc_final: 0.6779 (ptmt) REVERT: A 329 ARG cc_start: 0.7430 (tmm-80) cc_final: 0.5927 (tpp-160) REVERT: A 414 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5826 (tt0) REVERT: A 455 LEU cc_start: 0.8914 (mt) cc_final: 0.8641 (mt) REVERT: A 462 MET cc_start: 0.7846 (mmm) cc_final: 0.7426 (mmm) REVERT: H 88 TYR cc_start: 0.6812 (m-80) cc_final: 0.6450 (m-80) REVERT: I 118 TRP cc_start: 0.8257 (m100) cc_final: 0.8042 (m100) REVERT: J 3 GLN cc_start: 0.7287 (tp40) cc_final: 0.6985 (mm-40) REVERT: J 88 TYR cc_start: 0.6865 (m-80) cc_final: 0.6287 (m-80) REVERT: L 40 TYR cc_start: 0.7370 (m-80) cc_final: 0.7044 (m-80) REVERT: M 55 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6732 (t80) REVERT: B 210 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: B 259 LYS cc_start: 0.8146 (mttt) cc_final: 0.7632 (mtpp) REVERT: B 264 LYS cc_start: 0.7455 (mttt) cc_final: 0.6663 (ptmt) REVERT: B 329 ARG cc_start: 0.7563 (tmm-80) cc_final: 0.5895 (tpp-160) REVERT: B 367 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6810 (mm) REVERT: B 414 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5897 (tt0) REVERT: B 444 MET cc_start: 0.7384 (mmm) cc_final: 0.6297 (tmm) REVERT: B 455 LEU cc_start: 0.8954 (mt) cc_final: 0.8672 (mt) REVERT: B 462 MET cc_start: 0.8004 (mmm) cc_final: 0.7514 (mmm) REVERT: C 33 ARG cc_start: 0.7959 (mmm160) cc_final: 0.7352 (mmp-170) REVERT: C 210 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8044 (pm20) REVERT: C 264 LYS cc_start: 0.7680 (mttt) cc_final: 0.6984 (ptmt) REVERT: C 338 PHE cc_start: 0.7213 (t80) cc_final: 0.6843 (t80) outliers start: 74 outliers final: 53 residues processed: 261 average time/residue: 0.1208 time to fit residues: 50.9628 Evaluate side-chains 257 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 55 TYR Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 158 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 104 optimal weight: 0.0040 chunk 99 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 125 optimal weight: 0.0670 chunk 171 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 overall best weight: 0.5130 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.179570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145087 restraints weight = 21107.116| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.12 r_work: 0.3612 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17835 Z= 0.119 Angle : 0.622 9.755 24276 Z= 0.308 Chirality : 0.046 0.252 2751 Planarity : 0.004 0.050 3084 Dihedral : 8.627 59.935 3344 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.87 % Allowed : 13.29 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.97 (0.18), residues: 2130 helix: 1.52 (0.27), residues: 348 sheet: -0.38 (0.21), residues: 579 loop : -1.48 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.013 0.001 TYR H 103 PHE 0.013 0.001 PHE I 71 TRP 0.012 0.001 TRP I 55 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00271 (17763) covalent geometry : angle 0.60192 (24084) SS BOND : bond 0.00334 ( 24) SS BOND : angle 1.39477 ( 48) hydrogen bonds : bond 0.03192 ( 576) hydrogen bonds : angle 5.18672 ( 1512) link_BETA1-4 : bond 0.00657 ( 18) link_BETA1-4 : angle 2.13921 ( 54) link_NAG-ASN : bond 0.00475 ( 30) link_NAG-ASN : angle 1.86110 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 207 time to evaluate : 0.594 Fit side-chains REVERT: A 145 SER cc_start: 0.7575 (m) cc_final: 0.7007 (p) REVERT: A 264 LYS cc_start: 0.7382 (mttt) cc_final: 0.6688 (pttt) REVERT: A 329 ARG cc_start: 0.7375 (tmm-80) cc_final: 0.5882 (tpp-160) REVERT: A 444 MET cc_start: 0.7616 (tpt) cc_final: 0.7272 (tpt) REVERT: A 455 LEU cc_start: 0.8852 (mt) cc_final: 0.8596 (mt) REVERT: A 462 MET cc_start: 0.7817 (mmm) cc_final: 0.7360 (mmm) REVERT: H 88 TYR cc_start: 0.6731 (m-80) cc_final: 0.6348 (m-80) REVERT: J 3 GLN cc_start: 0.7234 (tp40) cc_final: 0.6941 (mm-40) REVERT: J 88 TYR cc_start: 0.6825 (m-80) cc_final: 0.6258 (m-80) REVERT: L 55 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.5213 (t80) REVERT: N 55 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.5787 (t80) REVERT: B 77 ASP cc_start: 0.7474 (m-30) cc_final: 0.7175 (m-30) REVERT: B 259 LYS cc_start: 0.8150 (mttt) cc_final: 0.7642 (mtpp) REVERT: B 329 ARG cc_start: 0.7379 (tmm-80) cc_final: 0.5836 (tpp-160) REVERT: B 367 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6500 (mm) REVERT: B 455 LEU cc_start: 0.8903 (mt) cc_final: 0.8646 (mt) REVERT: C 18 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.7394 (p-80) REVERT: C 33 ARG cc_start: 0.7935 (mmm160) cc_final: 0.7319 (mmp-170) REVERT: C 264 LYS cc_start: 0.7391 (mttt) cc_final: 0.6568 (ptmt) REVERT: C 329 ARG cc_start: 0.7081 (tmm-80) cc_final: 0.5609 (tpp-160) REVERT: C 338 PHE cc_start: 0.7315 (t80) cc_final: 0.6909 (t80) outliers start: 71 outliers final: 49 residues processed: 255 average time/residue: 0.1155 time to fit residues: 48.0699 Evaluate side-chains 250 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 55 TYR Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 138 optimal weight: 0.1980 chunk 141 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 153 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 121 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.182242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.148090 restraints weight = 21084.882| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.10 r_work: 0.3618 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17835 Z= 0.102 Angle : 0.592 9.784 24276 Z= 0.293 Chirality : 0.045 0.236 2751 Planarity : 0.004 0.049 3084 Dihedral : 8.391 57.899 3344 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.14 % Allowed : 13.40 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.75 (0.18), residues: 2130 helix: 1.88 (0.27), residues: 348 sheet: -0.27 (0.21), residues: 579 loop : -1.38 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 33 TYR 0.016 0.001 TYR M 40 PHE 0.014 0.001 PHE I 71 TRP 0.012 0.001 TRP I 55 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00225 (17763) covalent geometry : angle 0.57243 (24084) SS BOND : bond 0.00331 ( 24) SS BOND : angle 1.49948 ( 48) hydrogen bonds : bond 0.02929 ( 576) hydrogen bonds : angle 4.99946 ( 1512) link_BETA1-4 : bond 0.00645 ( 18) link_BETA1-4 : angle 2.05998 ( 54) link_NAG-ASN : bond 0.00457 ( 30) link_NAG-ASN : angle 1.73132 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 212 time to evaluate : 0.692 Fit side-chains REVERT: A 145 SER cc_start: 0.7674 (m) cc_final: 0.7134 (p) REVERT: A 312 SER cc_start: 0.8887 (m) cc_final: 0.8640 (p) REVERT: A 329 ARG cc_start: 0.7300 (tmm-80) cc_final: 0.5795 (tpp-160) REVERT: A 414 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5807 (tt0) REVERT: A 455 LEU cc_start: 0.8818 (mt) cc_final: 0.8569 (mt) REVERT: A 462 MET cc_start: 0.7864 (mmm) cc_final: 0.7412 (mmm) REVERT: H 88 TYR cc_start: 0.6636 (m-80) cc_final: 0.6304 (m-80) REVERT: J 3 GLN cc_start: 0.7266 (tp40) cc_final: 0.7010 (mm-40) REVERT: J 88 TYR cc_start: 0.6725 (m-80) cc_final: 0.6231 (m-80) REVERT: J 109 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7006 (mt) REVERT: L 55 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.5245 (t80) REVERT: M 55 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.6475 (t80) REVERT: N 55 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.5836 (t80) REVERT: B 77 ASP cc_start: 0.7390 (m-30) cc_final: 0.7068 (m-30) REVERT: B 259 LYS cc_start: 0.8032 (mttt) cc_final: 0.7528 (mtpp) REVERT: B 329 ARG cc_start: 0.7364 (tmm-80) cc_final: 0.5828 (tpp-160) REVERT: B 367 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6477 (mm) REVERT: B 414 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5716 (tt0) REVERT: B 444 MET cc_start: 0.7439 (mmm) cc_final: 0.6527 (tmm) REVERT: B 446 LYS cc_start: 0.6924 (ttmm) cc_final: 0.6660 (mtpt) REVERT: B 455 LEU cc_start: 0.8902 (mt) cc_final: 0.8626 (mt) REVERT: B 462 MET cc_start: 0.7630 (mmm) cc_final: 0.7159 (mmm) REVERT: C 18 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7489 (p-80) REVERT: C 33 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7459 (ptm-80) REVERT: C 145 SER cc_start: 0.7632 (m) cc_final: 0.7317 (p) REVERT: C 329 ARG cc_start: 0.6928 (tmm-80) cc_final: 0.5466 (tpp-160) REVERT: C 367 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6661 (mm) outliers start: 76 outliers final: 50 residues processed: 260 average time/residue: 0.1176 time to fit residues: 50.0995 Evaluate side-chains 263 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 55 TYR Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 55 TYR Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 67 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.176855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142941 restraints weight = 21206.102| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.00 r_work: 0.3553 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17835 Z= 0.202 Angle : 0.688 10.559 24276 Z= 0.342 Chirality : 0.049 0.319 2751 Planarity : 0.005 0.052 3084 Dihedral : 8.656 59.961 3342 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.03 % Allowed : 14.27 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.16 (0.18), residues: 2130 helix: 1.29 (0.27), residues: 357 sheet: -0.45 (0.21), residues: 579 loop : -1.64 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.019 0.002 TYR H 103 PHE 0.017 0.002 PHE I 71 TRP 0.016 0.002 TRP B 343 HIS 0.009 0.002 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00482 (17763) covalent geometry : angle 0.66499 (24084) SS BOND : bond 0.00495 ( 24) SS BOND : angle 2.16027 ( 48) hydrogen bonds : bond 0.03636 ( 576) hydrogen bonds : angle 5.13819 ( 1512) link_BETA1-4 : bond 0.00723 ( 18) link_BETA1-4 : angle 2.28384 ( 54) link_NAG-ASN : bond 0.00487 ( 30) link_NAG-ASN : angle 1.91310 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 212 time to evaluate : 0.672 Fit side-chains REVERT: A 145 SER cc_start: 0.7620 (m) cc_final: 0.7124 (p) REVERT: A 197 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7330 (mm-40) REVERT: A 264 LYS cc_start: 0.7461 (mttt) cc_final: 0.6714 (pttt) REVERT: A 329 ARG cc_start: 0.7457 (tmm-80) cc_final: 0.5925 (tpp-160) REVERT: A 359 GLU cc_start: 0.7993 (mp0) cc_final: 0.7745 (mp0) REVERT: A 414 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5807 (tt0) REVERT: A 455 LEU cc_start: 0.8857 (mt) cc_final: 0.8594 (mt) REVERT: A 462 MET cc_start: 0.7906 (mmm) cc_final: 0.7457 (mmm) REVERT: H 3 GLN cc_start: 0.7009 (tp40) cc_final: 0.6723 (mm-40) REVERT: H 88 TYR cc_start: 0.6764 (m-80) cc_final: 0.6419 (m-80) REVERT: J 3 GLN cc_start: 0.7262 (tp40) cc_final: 0.7043 (mm-40) REVERT: J 88 TYR cc_start: 0.6783 (m-80) cc_final: 0.6227 (m-80) REVERT: L 40 TYR cc_start: 0.7423 (m-80) cc_final: 0.7113 (m-80) REVERT: L 55 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.5083 (t80) REVERT: M 55 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.6508 (t80) REVERT: N 55 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5777 (t80) REVERT: B 77 ASP cc_start: 0.7487 (m-30) cc_final: 0.7140 (m-30) REVERT: B 259 LYS cc_start: 0.8070 (mttt) cc_final: 0.7565 (mtpp) REVERT: B 329 ARG cc_start: 0.7679 (tmm-80) cc_final: 0.6022 (tpp-160) REVERT: B 367 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6785 (mm) REVERT: B 414 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5819 (tt0) REVERT: B 455 LEU cc_start: 0.8936 (mt) cc_final: 0.8633 (mt) REVERT: B 462 MET cc_start: 0.7897 (mmm) cc_final: 0.7430 (mmm) REVERT: C 18 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7432 (p-80) REVERT: C 33 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7530 (ptm-80) REVERT: C 62 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7806 (pm20) REVERT: C 264 LYS cc_start: 0.7474 (mttt) cc_final: 0.6677 (ptmt) REVERT: C 329 ARG cc_start: 0.7126 (tmm-80) cc_final: 0.5789 (tpp-160) REVERT: C 367 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6705 (mm) outliers start: 74 outliers final: 56 residues processed: 260 average time/residue: 0.1110 time to fit residues: 46.8910 Evaluate side-chains 269 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 55 TYR Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 55 TYR Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 163 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 109 optimal weight: 0.3980 chunk 128 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.179290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145801 restraints weight = 21130.648| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.99 r_work: 0.3624 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17835 Z= 0.129 Angle : 0.627 9.721 24276 Z= 0.309 Chirality : 0.046 0.249 2751 Planarity : 0.004 0.050 3084 Dihedral : 8.479 59.987 3342 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.92 % Allowed : 14.65 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.95 (0.18), residues: 2130 helix: 1.70 (0.27), residues: 348 sheet: -0.33 (0.21), residues: 561 loop : -1.53 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.019 0.001 TYR M 40 PHE 0.016 0.001 PHE C 467 TRP 0.013 0.001 TRP I 55 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00299 (17763) covalent geometry : angle 0.60359 (24084) SS BOND : bond 0.00328 ( 24) SS BOND : angle 2.19024 ( 48) hydrogen bonds : bond 0.03132 ( 576) hydrogen bonds : angle 4.99891 ( 1512) link_BETA1-4 : bond 0.00659 ( 18) link_BETA1-4 : angle 2.08899 ( 54) link_NAG-ASN : bond 0.00455 ( 30) link_NAG-ASN : angle 1.81667 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 212 time to evaluate : 0.590 Fit side-chains REVERT: A 145 SER cc_start: 0.7635 (m) cc_final: 0.7091 (p) REVERT: A 264 LYS cc_start: 0.7432 (mttt) cc_final: 0.6696 (pttt) REVERT: A 312 SER cc_start: 0.8928 (m) cc_final: 0.8647 (p) REVERT: A 329 ARG cc_start: 0.7466 (tmm-80) cc_final: 0.5954 (tpp-160) REVERT: A 359 GLU cc_start: 0.8013 (mp0) cc_final: 0.7808 (mp0) REVERT: A 414 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5878 (tt0) REVERT: A 455 LEU cc_start: 0.8880 (mt) cc_final: 0.8637 (mt) REVERT: A 462 MET cc_start: 0.7907 (mmm) cc_final: 0.7426 (mmm) REVERT: H 3 GLN cc_start: 0.7020 (tp40) cc_final: 0.6750 (mm-40) REVERT: H 88 TYR cc_start: 0.6759 (m-80) cc_final: 0.6421 (m-80) REVERT: I 20 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6753 (ttpt) REVERT: J 88 TYR cc_start: 0.6811 (m-80) cc_final: 0.6265 (m-80) REVERT: L 55 TYR cc_start: 0.6890 (OUTLIER) cc_final: 0.5271 (t80) REVERT: M 55 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.6488 (t80) REVERT: N 55 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.5793 (t80) REVERT: B 77 ASP cc_start: 0.7434 (m-30) cc_final: 0.7131 (m-30) REVERT: B 329 ARG cc_start: 0.7569 (tmm-80) cc_final: 0.5937 (tpp-160) REVERT: B 367 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6758 (mm) REVERT: B 387 LYS cc_start: 0.8207 (mmmm) cc_final: 0.7535 (pttt) REVERT: B 414 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5786 (tt0) REVERT: B 444 MET cc_start: 0.7449 (mmm) cc_final: 0.6667 (tpt) REVERT: B 455 LEU cc_start: 0.8956 (mt) cc_final: 0.8664 (mt) REVERT: B 462 MET cc_start: 0.7722 (mmm) cc_final: 0.7249 (mmm) REVERT: C 18 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7447 (p-80) REVERT: C 33 ARG cc_start: 0.8013 (mmm160) cc_final: 0.7547 (ptm-80) REVERT: C 62 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7824 (pm20) REVERT: C 168 MET cc_start: 0.7545 (tpt) cc_final: 0.7199 (tpt) REVERT: C 264 LYS cc_start: 0.7395 (mttt) cc_final: 0.6577 (ptmt) REVERT: C 329 ARG cc_start: 0.7118 (tmm-80) cc_final: 0.5732 (tpp-160) REVERT: C 367 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6687 (mm) outliers start: 72 outliers final: 57 residues processed: 257 average time/residue: 0.1081 time to fit residues: 44.8252 Evaluate side-chains 274 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 55 TYR Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 55 TYR Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 185 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 105 optimal weight: 0.3980 chunk 158 optimal weight: 0.6980 chunk 179 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 189 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.180790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.147087 restraints weight = 21128.280| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 3.06 r_work: 0.3629 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17835 Z= 0.114 Angle : 0.606 9.733 24276 Z= 0.299 Chirality : 0.045 0.241 2751 Planarity : 0.004 0.051 3084 Dihedral : 8.298 58.041 3342 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.70 % Allowed : 14.92 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.80 (0.18), residues: 2130 helix: 1.96 (0.27), residues: 348 sheet: -0.24 (0.22), residues: 561 loop : -1.47 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.017 0.001 TYR M 40 PHE 0.017 0.001 PHE C 467 TRP 0.013 0.001 TRP I 55 HIS 0.004 0.001 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00261 (17763) covalent geometry : angle 0.58482 (24084) SS BOND : bond 0.00297 ( 24) SS BOND : angle 2.03233 ( 48) hydrogen bonds : bond 0.02965 ( 576) hydrogen bonds : angle 4.86621 ( 1512) link_BETA1-4 : bond 0.00630 ( 18) link_BETA1-4 : angle 2.03859 ( 54) link_NAG-ASN : bond 0.00442 ( 30) link_NAG-ASN : angle 1.73081 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 207 time to evaluate : 0.696 Fit side-chains REVERT: A 145 SER cc_start: 0.7593 (m) cc_final: 0.7064 (p) REVERT: A 312 SER cc_start: 0.8888 (m) cc_final: 0.8658 (p) REVERT: A 329 ARG cc_start: 0.7403 (tmm-80) cc_final: 0.5881 (tpp-160) REVERT: A 414 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5843 (tt0) REVERT: A 455 LEU cc_start: 0.8837 (mt) cc_final: 0.8583 (mt) REVERT: A 462 MET cc_start: 0.7800 (mmm) cc_final: 0.7340 (mmm) REVERT: H 3 GLN cc_start: 0.6921 (tp40) cc_final: 0.6666 (mm-40) REVERT: H 88 TYR cc_start: 0.6744 (m-80) cc_final: 0.6433 (m-80) REVERT: I 20 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6698 (ttpt) REVERT: J 88 TYR cc_start: 0.6760 (m-80) cc_final: 0.6251 (m-80) REVERT: L 55 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5146 (t80) REVERT: L 66 ASN cc_start: 0.7941 (m-40) cc_final: 0.7693 (m-40) REVERT: M 55 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.6416 (t80) REVERT: N 55 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5722 (t80) REVERT: B 77 ASP cc_start: 0.7347 (m-30) cc_final: 0.7011 (m-30) REVERT: B 329 ARG cc_start: 0.7473 (tmm-80) cc_final: 0.5900 (tpp-160) REVERT: B 367 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6778 (mm) REVERT: B 387 LYS cc_start: 0.8166 (mmmm) cc_final: 0.7499 (pttt) REVERT: B 414 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5740 (tt0) REVERT: B 444 MET cc_start: 0.7454 (mmm) cc_final: 0.6651 (tpt) REVERT: B 455 LEU cc_start: 0.8921 (mt) cc_final: 0.8636 (mt) REVERT: B 462 MET cc_start: 0.7652 (mmm) cc_final: 0.7162 (mmm) REVERT: C 18 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7489 (p-80) REVERT: C 33 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7498 (ptm-80) REVERT: C 62 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7824 (pm20) REVERT: C 145 SER cc_start: 0.7669 (m) cc_final: 0.7360 (p) REVERT: C 168 MET cc_start: 0.7474 (tpt) cc_final: 0.7146 (tpt) REVERT: C 329 ARG cc_start: 0.7077 (tmm-80) cc_final: 0.5573 (tpp-160) REVERT: C 367 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6669 (mm) outliers start: 68 outliers final: 55 residues processed: 252 average time/residue: 0.1160 time to fit residues: 47.3601 Evaluate side-chains 264 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 55 TYR Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 55 TYR Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 127 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 114 optimal weight: 0.0070 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 173 optimal weight: 0.2980 chunk 76 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.180208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.146202 restraints weight = 21004.724| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.09 r_work: 0.3631 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17835 Z= 0.122 Angle : 0.616 9.710 24276 Z= 0.304 Chirality : 0.045 0.247 2751 Planarity : 0.004 0.051 3084 Dihedral : 8.262 58.448 3340 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.81 % Allowed : 14.87 % Favored : 81.32 % 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: -0.80 (0.18), residues: 2130 helix: 1.99 (0.27), residues: 348 sheet: -0.29 (0.21), residues: 567 loop : -1.47 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.016 0.001 TYR M 40 PHE 0.011 0.001 PHE A 467 TRP 0.012 0.001 TRP I 55 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00283 (17763) covalent geometry : angle 0.59564 (24084) SS BOND : bond 0.00356 ( 24) SS BOND : angle 2.01075 ( 48) hydrogen bonds : bond 0.03000 ( 576) hydrogen bonds : angle 4.83763 ( 1512) link_BETA1-4 : bond 0.00623 ( 18) link_BETA1-4 : angle 2.02796 ( 54) link_NAG-ASN : bond 0.00442 ( 30) link_NAG-ASN : angle 1.71492 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 202 time to evaluate : 0.681 Fit side-chains REVERT: A 145 SER cc_start: 0.7654 (m) cc_final: 0.7100 (p) REVERT: A 312 SER cc_start: 0.8879 (m) cc_final: 0.8661 (p) REVERT: A 329 ARG cc_start: 0.7501 (tmm-80) cc_final: 0.6016 (tpp-160) REVERT: A 414 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5919 (tt0) REVERT: A 454 GLN cc_start: 0.7811 (mt0) cc_final: 0.7571 (mt0) REVERT: A 455 LEU cc_start: 0.8877 (mt) cc_final: 0.8629 (mt) REVERT: A 462 MET cc_start: 0.7863 (mmm) cc_final: 0.7416 (mmm) REVERT: H 3 GLN cc_start: 0.6983 (tp40) cc_final: 0.6747 (mm-40) REVERT: H 88 TYR cc_start: 0.6794 (m-80) cc_final: 0.6439 (m-80) REVERT: I 20 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6842 (ttpt) REVERT: J 88 TYR cc_start: 0.6838 (m-80) cc_final: 0.6328 (m-80) REVERT: L 55 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.5281 (t80) REVERT: L 66 ASN cc_start: 0.8090 (m-40) cc_final: 0.7835 (m-40) REVERT: M 55 TYR cc_start: 0.6907 (OUTLIER) cc_final: 0.6535 (t80) REVERT: N 55 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.5873 (t80) REVERT: B 77 ASP cc_start: 0.7363 (m-30) cc_final: 0.7018 (m-30) REVERT: B 210 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: B 329 ARG cc_start: 0.7571 (tmm-80) cc_final: 0.6017 (tpp-160) REVERT: B 367 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6848 (mm) REVERT: B 387 LYS cc_start: 0.8152 (mmmm) cc_final: 0.7454 (pttt) REVERT: B 414 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.5824 (tt0) REVERT: B 444 MET cc_start: 0.7495 (mmm) cc_final: 0.6685 (tpt) REVERT: B 455 LEU cc_start: 0.8972 (mt) cc_final: 0.8682 (mt) REVERT: B 462 MET cc_start: 0.7709 (mmm) cc_final: 0.7227 (mmm) REVERT: C 18 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7498 (p-80) REVERT: C 33 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7575 (ptm-80) REVERT: C 62 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7894 (pm20) REVERT: C 145 SER cc_start: 0.7679 (m) cc_final: 0.7354 (p) REVERT: C 210 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: C 329 ARG cc_start: 0.7209 (tmm-80) cc_final: 0.5733 (tpp-160) REVERT: C 367 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6764 (mm) outliers start: 70 outliers final: 57 residues processed: 248 average time/residue: 0.0988 time to fit residues: 39.8406 Evaluate side-chains 265 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 197 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 20 LYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 91 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 55 TYR Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 55 TYR Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 104 CYS Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 181 optimal weight: 0.0770 chunk 123 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.180038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145975 restraints weight = 21258.967| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.10 r_work: 0.3622 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17835 Z= 0.125 Angle : 0.615 9.692 24276 Z= 0.304 Chirality : 0.046 0.248 2751 Planarity : 0.004 0.051 3084 Dihedral : 8.253 58.220 3340 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.98 % Allowed : 14.87 % Favored : 81.15 % 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: -0.77 (0.18), residues: 2130 helix: 2.00 (0.27), residues: 348 sheet: -0.14 (0.22), residues: 549 loop : -1.50 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.016 0.001 TYR M 40 PHE 0.011 0.001 PHE A 467 TRP 0.012 0.001 TRP I 55 HIS 0.007 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00290 (17763) covalent geometry : angle 0.59438 (24084) SS BOND : bond 0.00362 ( 24) SS BOND : angle 1.97164 ( 48) hydrogen bonds : bond 0.03011 ( 576) hydrogen bonds : angle 4.81629 ( 1512) link_BETA1-4 : bond 0.00649 ( 18) link_BETA1-4 : angle 2.01340 ( 54) link_NAG-ASN : bond 0.00437 ( 30) link_NAG-ASN : angle 1.70776 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3784.43 seconds wall clock time: 65 minutes 55.92 seconds (3955.92 seconds total)