Starting phenix.real_space_refine on Sat Jul 4 00:29:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fk5_29248/07_2026/8fk5_29248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fk5_29248/07_2026/8fk5_29248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fk5_29248/07_2026/8fk5_29248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fk5_29248/07_2026/8fk5_29248.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fk5_29248/07_2026/8fk5_29248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fk5_29248/07_2026/8fk5_29248.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fk5_29248/07_2026/8fk5_29248.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fk5_29248/07_2026/8fk5_29248.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.062 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 117 5.16 5 C 10559 2.51 5 N 2802 2.21 5 O 3502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16980 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1102 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} 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 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 chiralities: 2 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" 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 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 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 chiralities: 2 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "R" 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 chiralities: 2 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 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 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 chiralities: 2 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "W" 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 chiralities: 2 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Y" 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 chiralities: 2 Chain: "Z" 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 chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "b" 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 chiralities: 2 Chain: "c" 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 chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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 chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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 chiralities: 2 Chain: "G" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 3.23, per 1000 atoms: 0.19 Number of scatterers: 16980 At special positions: 0 Unit cell: (131.043, 125.628, 166.782, 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 117 16.00 O 3502 8.00 N 2802 7.00 C 10559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN Q 4 " - " MAN Q 5 " " MAN X 4 " - " MAN X 5 " " MAN e 5 " - " MAN e 6 " " MAN e 8 " - " MAN e 9 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA a 3 " - " MAN a 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 8 " " MAN e 4 " - " MAN e 7 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA Q 3 " - " MAN Q 6 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 6 " " BMA a 3 " - " MAN a 5 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG A 703 " - " ASN A 618 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG C 611 " - " ASN C 137 " " NAG D 1 " - " ASN C 160 " " NAG E 1 " - " ASN C 197 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 332 " " NAG G 607 " - " ASN G 339 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 137 " " NAG G 611 " - " ASN G 276 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 234 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 332 " " NAG I 606 " - " ASN I 339 " " NAG I 607 " - " ASN I 355 " " NAG I 608 " - " ASN I 392 " " NAG I 609 " - " ASN I 137 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 276 " " NAG M 1 " - " ASN C 295 " " NAG N 1 " - " ASN C 363 " " NAG O 1 " - " ASN C 386 " " NAG P 1 " - " ASN G 197 " " NAG Q 1 " - " ASN G 262 " " NAG R 1 " - " ASN G 295 " " NAG S 1 " - " ASN G 363 " " NAG T 1 " - " ASN G 386 " " NAG U 1 " - " ASN G 448 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN I 197 " " NAG X 1 " - " ASN I 262 " " NAG Y 1 " - " ASN I 276 " " NAG Z 1 " - " ASN I 295 " " NAG a 1 " - " ASN I 363 " " NAG b 1 " - " ASN I 386 " " NAG c 1 " - " ASN I 448 " " NAG d 1 " - " ASN I 156 " " NAG e 1 " - " ASN I 160 " Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 692.8 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 30 sheets defined 24.6% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.543A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 535 removed outlier: 4.158A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 542 removed outlier: 4.063A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 removed outlier: 3.552A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 664 removed outlier: 3.585A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.317A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.779A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.367A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 3.758A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.930A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.504A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 64 removed outlier: 4.374A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 353 removed outlier: 3.587A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.630A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.018A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.267A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.547A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.071A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.570A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 98 through 115 removed outlier: 4.041A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.577A pdb=" N ARG G 151 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.821A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.504A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 474 through 484 removed outlier: 3.945A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 63 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.223A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 3.614A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 475 through 481 removed outlier: 4.113A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.550A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.102A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 4.871A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.517A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.820A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.306A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA8, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 309 removed outlier: 4.020A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR C 303 " --> pdb=" O ASP C 321A" (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP C 321A" --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'F' and resid 603 through 609 removed outlier: 4.314A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR I 499 " --> pdb=" O TRP I 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.388A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.652A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.779A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.469A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 260 current: chain 'G' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 287 current: chain 'G' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 393 through 395 current: chain 'G' and resid 465 through 470 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 374 through 378 removed outlier: 4.003A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 304 through 312 removed outlier: 3.501A pdb=" N ILE G 309 " --> pdb=" O GLN G 315 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.786A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 75 through 76 removed outlier: 4.078A pdb=" N VAL I 75 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.741A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 130 through 133 removed outlier: 4.705A pdb=" N PHE H 100J" --> pdb=" O LYS I 171 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N TYR I 173 " --> pdb=" O PHE H 100J" (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AC5, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.477A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET I 434 " --> pdb=" O ILE I 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 292 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 292 current: chain 'I' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 393 through 395 current: chain 'I' and resid 466 through 470 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 374 through 378 removed outlier: 4.543A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 301 through 312 removed outlier: 3.985A pdb=" N ASN I 301 " --> pdb=" O ILE I 323 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR I 320 " --> pdb=" O LYS I 305 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE I 309 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA I 316 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.713A pdb=" N ARG H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER H 25 " --> pdb=" O ARG H 3 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100O through 103 Processing sheet with id=AD2, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'L' and resid 19 through 24 484 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2659 1.32 - 1.45: 4959 1.45 - 1.57: 9526 1.57 - 1.70: 2 1.70 - 1.83: 154 Bond restraints: 17300 Sorted by residual: bond pdb=" C1 MAN e 9 " pdb=" O5 MAN e 9 " ideal model delta sigma weight residual 1.399 1.552 -0.153 2.00e-02 2.50e+03 5.82e+01 bond pdb=" C1 MAN e 9 " pdb=" C2 MAN e 9 " ideal model delta sigma weight residual 1.526 1.667 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" OH TYS H 100G" pdb=" S TYS H 100G" ideal model delta sigma weight residual 1.679 1.573 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.587 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" CZ TYS H 100G" pdb=" OH TYS H 100G" ideal model delta sigma weight residual 1.371 1.432 -0.061 2.00e-02 2.50e+03 9.33e+00 ... (remaining 17295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 23054 2.51 - 5.02: 365 5.02 - 7.52: 58 7.52 - 10.03: 2 10.03 - 12.54: 1 Bond angle restraints: 23480 Sorted by residual: angle pdb=" N THR I 467 " pdb=" CA THR I 467 " pdb=" C THR I 467 " ideal model delta sigma weight residual 108.23 120.77 -12.54 1.72e+00 3.38e-01 5.32e+01 angle pdb=" C THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta sigma weight residual 111.05 119.59 -8.54 1.69e+00 3.50e-01 2.55e+01 angle pdb=" N THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta sigma weight residual 110.24 116.75 -6.51 1.45e+00 4.76e-01 2.02e+01 angle pdb=" CA TYS H 100H" pdb=" C TYS H 100H" pdb=" O TYS H 100H" ideal model delta sigma weight residual 120.80 113.20 7.60 1.70e+00 3.46e-01 2.00e+01 angle pdb=" N ASP I 457 " pdb=" CA ASP I 457 " pdb=" C ASP I 457 " ideal model delta sigma weight residual 110.28 104.19 6.09 1.48e+00 4.57e-01 1.69e+01 ... (remaining 23475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8685 17.93 - 35.86: 657 35.86 - 53.79: 147 53.79 - 71.72: 36 71.72 - 89.65: 13 Dihedral angle restraints: 9538 sinusoidal: 3862 harmonic: 5676 Sorted by residual: dihedral pdb=" C THR I 467 " pdb=" N THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta harmonic sigma weight residual -122.00 -160.68 38.68 0 2.50e+00 1.60e-01 2.39e+02 dihedral pdb=" N THR I 467 " pdb=" C THR I 467 " pdb=" CA THR I 467 " pdb=" CB THR I 467 " ideal model delta harmonic sigma weight residual 123.40 160.13 -36.73 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" CB CYS I 378 " pdb=" SG CYS I 378 " pdb=" SG CYS I 445 " pdb=" CB CYS I 445 " ideal model delta sinusoidal sigma weight residual -86.00 -159.37 73.37 1 1.00e+01 1.00e-02 6.85e+01 ... (remaining 9535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 2956 0.331 - 0.661: 2 0.661 - 0.992: 0 0.992 - 1.323: 0 1.323 - 1.653: 1 Chirality restraints: 2959 Sorted by residual: chirality pdb=" CA THR I 467 " pdb=" N THR I 467 " pdb=" C THR I 467 " pdb=" CB THR I 467 " both_signs ideal model delta sigma weight residual False 2.53 0.87 1.65 2.00e-01 2.50e+01 6.83e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN G 448 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.41e+00 chirality pdb=" C1 MAN e 9 " pdb=" O2 MAN e 8 " pdb=" C2 MAN e 9 " pdb=" O5 MAN e 9 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 5.34e+00 ... (remaining 2956 not shown) Planarity restraints: 2901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG I 456 " 0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ARG I 456 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG I 456 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP I 457 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYS H 100H" 0.012 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C TYS H 100H" -0.045 2.00e-02 2.50e+03 pdb=" O TYS H 100H" 0.016 2.00e-02 2.50e+03 pdb=" N ASP H 100I" 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 3 " -0.165 9.50e-02 1.11e+02 7.42e-02 3.38e+00 pdb=" NE ARG H 3 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG H 3 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 3 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 3 " -0.006 2.00e-02 2.50e+03 ... (remaining 2898 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 203 2.62 - 3.19: 15011 3.19 - 3.76: 23718 3.76 - 4.33: 34615 4.33 - 4.90: 57220 Nonbonded interactions: 130767 Sorted by model distance: nonbonded pdb=" O ASP A 632 " pdb=" OG SER A 636 " model vdw 2.052 3.040 nonbonded pdb=" OD1 ASP C 457 " pdb=" OG1 THR C 467 " model vdw 2.090 3.040 nonbonded pdb=" NH2 ARG G 350 " pdb=" O ASN G 398 " model vdw 2.168 3.120 nonbonded pdb=" OG1 THR B 627 " pdb=" OE1 GLN B 630 " model vdw 2.168 3.040 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.198 3.040 ... (remaining 130762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 519 through 702) selection = chain 'B' selection = (chain 'F' and (resid 519 through 546 or resid 569 through 702)) } ncs_group { reference = (chain 'C' and resid 33 through 609) selection = (chain 'G' and resid 33 through 609) selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'X' } ncs_group { reference = chain 'V' selection = chain 'a' selection = chain 'd' } 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: 3.880 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.000 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 17449 Z= 0.259 Angle : 0.755 12.540 23890 Z= 0.333 Chirality : 0.059 1.653 2959 Planarity : 0.003 0.074 2840 Dihedral : 13.705 89.653 5763 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1932 helix: 0.93 (0.29), residues: 369 sheet: 0.69 (0.24), residues: 505 loop : -0.15 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 585 TYR 0.008 0.001 TYR L 49 PHE 0.006 0.001 PHE C 53 TRP 0.019 0.001 TRP C 479 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.26 (17300) covalent geometry : angle 0.72261 / 0.33 (23480) SS BOND : bond 0.00183 / 0.11 ( 37) SS BOND : angle 0.98692 / 0.59 ( 74) hydrogen bonds : bond 0.24659 / 16.19 ( 484) hydrogen bonds : angle 8.15189 / 5.84 ( 1314) link_ALPHA1-2 : bond 0.02570 / 1.76 ( 5) link_ALPHA1-2 : angle 2.79397 / 1.91 ( 15) link_ALPHA1-3 : bond 0.00838 / 0.40 ( 8) link_ALPHA1-3 : angle 2.29375 / 1.41 ( 24) link_ALPHA1-6 : bond 0.00715 / 0.33 ( 8) link_ALPHA1-6 : angle 1.61108 / 0.98 ( 24) link_BETA1-4 : bond 0.00468 / 0.29 ( 30) link_BETA1-4 : angle 1.98412 / 1.27 ( 90) link_NAG-ASN : bond 0.00299 / 0.15 ( 61) link_NAG-ASN : angle 1.82595 / 1.24 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.8904 (t) cc_final: 0.8561 (p) REVERT: C 38 VAL cc_start: 0.8998 (p) cc_final: 0.8605 (m) REVERT: C 46 LYS cc_start: 0.8449 (pttp) cc_final: 0.8215 (pttp) REVERT: G 39 TYR cc_start: 0.8834 (m-80) cc_final: 0.8568 (m-80) REVERT: H 94 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7246 (ttt180) REVERT: L 36 TYR cc_start: 0.7830 (m-80) cc_final: 0.7506 (m-80) outliers start: 2 outliers final: 0 residues processed: 331 average time/residue: 0.1240 time to fit residues: 60.2893 Evaluate side-chains 189 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN A 651 ASN B 540 GLN B 543 ASN C 249 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN G 249 HIS G 374 HIS I 99 ASN I 374 HIS H 100CASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.174973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.144335 restraints weight = 20622.560| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.29 r_work: 0.3501 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17449 Z= 0.212 Angle : 0.768 17.717 23890 Z= 0.360 Chirality : 0.049 0.348 2959 Planarity : 0.005 0.050 2840 Dihedral : 4.726 25.478 2107 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.08 % Allowed : 7.16 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1932 helix: 0.76 (0.27), residues: 385 sheet: 0.45 (0.22), residues: 513 loop : -0.40 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 360 TYR 0.017 0.002 TYR F 643 PHE 0.033 0.002 PHE C 53 TRP 0.021 0.002 TRP C 479 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (17300) covalent geometry : angle 0.72008 / 0.35 (23480) SS BOND : bond 0.00457 / 0.29 ( 37) SS BOND : angle 1.68794 / 1.06 ( 74) hydrogen bonds : bond 0.05793 / 3.82 ( 484) hydrogen bonds : angle 5.59750 / 4.07 ( 1314) link_ALPHA1-2 : bond 0.00758 / 0.36 ( 5) link_ALPHA1-2 : angle 2.13582 / 1.23 ( 15) link_ALPHA1-3 : bond 0.00473 / 0.22 ( 8) link_ALPHA1-3 : angle 1.62032 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00542 / 0.27 ( 8) link_ALPHA1-6 : angle 1.53892 / 0.96 ( 24) link_BETA1-4 : bond 0.00531 / 0.37 ( 30) link_BETA1-4 : angle 1.57930 / 1.01 ( 90) link_NAG-ASN : bond 0.00446 / 0.24 ( 61) link_NAG-ASN : angle 2.66096 / 1.89 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 THR cc_start: 0.8375 (m) cc_final: 0.8047 (t) REVERT: A 584 GLU cc_start: 0.8446 (pt0) cc_final: 0.8101 (mt-10) REVERT: B 536 THR cc_start: 0.9087 (t) cc_final: 0.8789 (p) REVERT: B 542 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7815 (mtm-85) REVERT: B 654 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6649 (mt-10) REVERT: C 347 LYS cc_start: 0.8183 (tttp) cc_final: 0.7964 (mtpt) REVERT: C 349 LEU cc_start: 0.8411 (mt) cc_final: 0.8200 (mt) REVERT: G 100 MET cc_start: 0.8854 (mtp) cc_final: 0.8529 (mtp) REVERT: G 151 ARG cc_start: 0.9019 (ttm-80) cc_final: 0.8299 (ttm110) REVERT: G 485 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7663 (tttp) REVERT: I 115 SER cc_start: 0.9069 (t) cc_final: 0.8853 (p) REVERT: I 246 GLN cc_start: 0.7623 (pm20) cc_final: 0.7383 (pm20) REVERT: H 38 ARG cc_start: 0.7516 (ptt180) cc_final: 0.7303 (ptt180) REVERT: H 72 ASP cc_start: 0.8302 (t0) cc_final: 0.8077 (t0) REVERT: H 94 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7878 (ttt-90) REVERT: L 36 TYR cc_start: 0.7999 (m-80) cc_final: 0.7542 (m-80) outliers start: 36 outliers final: 24 residues processed: 236 average time/residue: 0.1221 time to fit residues: 42.8873 Evaluate side-chains 207 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 34 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 108 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 GLN C 478 ASN I 99 ASN H 100CASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.175380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144696 restraints weight = 20889.147| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.30 r_work: 0.3505 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17449 Z= 0.139 Angle : 0.658 18.395 23890 Z= 0.306 Chirality : 0.045 0.378 2959 Planarity : 0.004 0.045 2840 Dihedral : 4.550 31.531 2107 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.48 % Allowed : 9.53 % Favored : 87.98 % 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 are not related in a simple way. whole: 0.13 (0.19), residues: 1932 helix: 0.93 (0.27), residues: 390 sheet: 0.47 (0.23), residues: 516 loop : -0.39 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 617 TYR 0.015 0.001 TYR C 484 PHE 0.025 0.001 PHE C 53 TRP 0.019 0.001 TRP I 35 HIS 0.007 0.001 HIS H 100R Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (17300) covalent geometry : angle 0.60496 / 0.29 (23480) SS BOND : bond 0.00299 / 0.21 ( 37) SS BOND : angle 1.52038 / 0.91 ( 74) hydrogen bonds : bond 0.05018 / 3.31 ( 484) hydrogen bonds : angle 5.11370 / 3.71 ( 1314) link_ALPHA1-2 : bond 0.00822 / 0.44 ( 5) link_ALPHA1-2 : angle 1.64725 / 0.98 ( 15) link_ALPHA1-3 : bond 0.00689 / 0.32 ( 8) link_ALPHA1-3 : angle 1.36023 / 0.81 ( 24) link_ALPHA1-6 : bond 0.00529 / 0.24 ( 8) link_ALPHA1-6 : angle 1.46246 / 0.89 ( 24) link_BETA1-4 : bond 0.00488 / 0.32 ( 30) link_BETA1-4 : angle 1.34564 / 0.87 ( 90) link_NAG-ASN : bond 0.00480 / 0.24 ( 61) link_NAG-ASN : angle 2.63274 / 1.90 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.9072 (t) cc_final: 0.8764 (p) REVERT: C 95 MET cc_start: 0.8729 (ptm) cc_final: 0.7833 (ttp) REVERT: C 205 CYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6827 (m) REVERT: C 349 LEU cc_start: 0.8308 (mt) cc_final: 0.8079 (mt) REVERT: F 617 ARG cc_start: 0.7837 (ttm110) cc_final: 0.7589 (ttm170) REVERT: G 100 MET cc_start: 0.8844 (mtp) cc_final: 0.8515 (mtp) REVERT: G 151 ARG cc_start: 0.9045 (ttm-80) cc_final: 0.8200 (ttp80) REVERT: G 485 LYS cc_start: 0.8052 (ttmt) cc_final: 0.7577 (tttp) REVERT: I 115 SER cc_start: 0.9070 (t) cc_final: 0.8819 (p) REVERT: I 205 CYS cc_start: 0.6704 (OUTLIER) cc_final: 0.6391 (m) REVERT: I 246 GLN cc_start: 0.7583 (pm20) cc_final: 0.7162 (pm20) REVERT: H 72 ASP cc_start: 0.8300 (t0) cc_final: 0.8071 (t0) REVERT: H 94 ARG cc_start: 0.8152 (ttp-170) cc_final: 0.7839 (ttt-90) REVERT: L 24 GLN cc_start: 0.6878 (tm-30) cc_final: 0.6469 (mt0) REVERT: L 36 TYR cc_start: 0.7928 (m-80) cc_final: 0.7501 (m-80) outliers start: 43 outliers final: 31 residues processed: 231 average time/residue: 0.1238 time to fit residues: 42.6338 Evaluate side-chains 215 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 21 optimal weight: 0.5980 chunk 157 optimal weight: 0.0070 chunk 101 optimal weight: 1.9990 chunk 134 optimal weight: 0.0570 chunk 193 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 ASN C 82 GLN G 422 GLN H 100CASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.176098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145540 restraints weight = 20767.826| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.29 r_work: 0.3513 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17449 Z= 0.117 Angle : 0.629 18.451 23890 Z= 0.291 Chirality : 0.044 0.424 2959 Planarity : 0.003 0.042 2840 Dihedral : 4.394 27.886 2107 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.89 % Allowed : 10.17 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1932 helix: 1.02 (0.28), residues: 390 sheet: 0.48 (0.23), residues: 517 loop : -0.35 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 500 TYR 0.011 0.001 TYR L 49 PHE 0.020 0.001 PHE C 53 TRP 0.013 0.001 TRP I 35 HIS 0.005 0.001 HIS H 100R Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (17300) covalent geometry : angle 0.57900 / 0.28 (23480) SS BOND : bond 0.00260 / 0.17 ( 37) SS BOND : angle 1.23012 / 0.69 ( 74) hydrogen bonds : bond 0.04382 / 2.89 ( 484) hydrogen bonds : angle 4.86335 / 3.53 ( 1314) link_ALPHA1-2 : bond 0.00761 / 0.40 ( 5) link_ALPHA1-2 : angle 1.65399 / 0.96 ( 15) link_ALPHA1-3 : bond 0.00644 / 0.30 ( 8) link_ALPHA1-3 : angle 1.35269 / 0.81 ( 24) link_ALPHA1-6 : bond 0.00524 / 0.24 ( 8) link_ALPHA1-6 : angle 1.45315 / 0.88 ( 24) link_BETA1-4 : bond 0.00449 / 0.29 ( 30) link_BETA1-4 : angle 1.28810 / 0.84 ( 90) link_NAG-ASN : bond 0.00454 / 0.22 ( 61) link_NAG-ASN : angle 2.54867 / 1.85 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 LYS cc_start: 0.7009 (tptp) cc_final: 0.6700 (tptt) REVERT: B 536 THR cc_start: 0.9074 (t) cc_final: 0.8742 (p) REVERT: C 46 LYS cc_start: 0.8676 (pttm) cc_final: 0.8447 (pttp) REVERT: C 95 MET cc_start: 0.8788 (ptm) cc_final: 0.7918 (ttp) REVERT: C 205 CYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6845 (m) REVERT: C 349 LEU cc_start: 0.8263 (mt) cc_final: 0.8029 (mt) REVERT: G 100 MET cc_start: 0.8865 (mtp) cc_final: 0.8534 (mtp) REVERT: G 151 ARG cc_start: 0.9039 (ttm-80) cc_final: 0.8184 (ttp80) REVERT: I 115 SER cc_start: 0.9081 (t) cc_final: 0.8792 (p) REVERT: I 205 CYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6481 (m) REVERT: I 246 GLN cc_start: 0.7528 (pm20) cc_final: 0.7085 (pm20) REVERT: H 72 ASP cc_start: 0.8361 (t0) cc_final: 0.8121 (t0) REVERT: H 94 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7868 (ttt-90) REVERT: L 24 GLN cc_start: 0.7032 (tm-30) cc_final: 0.6588 (mt0) REVERT: L 36 TYR cc_start: 0.7927 (m-80) cc_final: 0.7542 (m-80) outliers start: 50 outliers final: 32 residues processed: 229 average time/residue: 0.1163 time to fit residues: 39.5671 Evaluate side-chains 220 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 68 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 103 GLN I 422 GLN H 100CASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.171896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141110 restraints weight = 20777.372| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.29 r_work: 0.3464 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17449 Z= 0.170 Angle : 0.677 18.376 23890 Z= 0.312 Chirality : 0.046 0.444 2959 Planarity : 0.004 0.041 2840 Dihedral : 4.542 27.725 2107 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.52 % Allowed : 10.57 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.19), residues: 1932 helix: 0.98 (0.28), residues: 390 sheet: 0.39 (0.22), residues: 533 loop : -0.44 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 298 TYR 0.015 0.001 TYR G 173 PHE 0.023 0.002 PHE C 53 TRP 0.012 0.001 TRP I 35 HIS 0.005 0.001 HIS H 100R Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (17300) covalent geometry : angle 0.62792 / 0.30 (23480) SS BOND : bond 0.00327 / 0.22 ( 37) SS BOND : angle 1.34975 / 0.77 ( 74) hydrogen bonds : bond 0.04555 / 2.97 ( 484) hydrogen bonds : angle 4.85001 / 3.52 ( 1314) link_ALPHA1-2 : bond 0.00708 / 0.37 ( 5) link_ALPHA1-2 : angle 1.73675 / 0.96 ( 15) link_ALPHA1-3 : bond 0.00624 / 0.29 ( 8) link_ALPHA1-3 : angle 1.39546 / 0.84 ( 24) link_ALPHA1-6 : bond 0.00453 / 0.21 ( 8) link_ALPHA1-6 : angle 1.55359 / 0.95 ( 24) link_BETA1-4 : bond 0.00456 / 0.30 ( 30) link_BETA1-4 : angle 1.34754 / 0.89 ( 90) link_NAG-ASN : bond 0.00502 / 0.26 ( 61) link_NAG-ASN : angle 2.60401 / 1.88 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 202 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.9109 (t) cc_final: 0.8737 (p) REVERT: C 292 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8841 (m) REVERT: G 151 ARG cc_start: 0.9008 (ttm-80) cc_final: 0.8148 (ttp80) REVERT: G 423 ILE cc_start: 0.8806 (mm) cc_final: 0.8561 (mt) REVERT: I 115 SER cc_start: 0.9191 (t) cc_final: 0.8846 (p) REVERT: I 205 CYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6529 (m) REVERT: I 246 GLN cc_start: 0.7523 (pm20) cc_final: 0.7058 (pm20) REVERT: H 72 ASP cc_start: 0.8388 (t0) cc_final: 0.8060 (t0) REVERT: H 94 ARG cc_start: 0.8091 (ttp-170) cc_final: 0.7803 (ttt-90) REVERT: H 100 TYR cc_start: 0.8545 (m-80) cc_final: 0.8045 (m-80) REVERT: L 24 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6806 (mt0) outliers start: 61 outliers final: 44 residues processed: 246 average time/residue: 0.1126 time to fit residues: 41.4707 Evaluate side-chains 236 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 605 CYS Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 101 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.167085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.136109 restraints weight = 20832.711| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.28 r_work: 0.3392 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17449 Z= 0.252 Angle : 0.760 18.408 23890 Z= 0.353 Chirality : 0.049 0.453 2959 Planarity : 0.004 0.044 2840 Dihedral : 4.985 34.080 2107 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.10 % Allowed : 10.98 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1932 helix: 0.72 (0.28), residues: 387 sheet: 0.17 (0.23), residues: 504 loop : -0.77 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 585 TYR 0.020 0.002 TYR L 49 PHE 0.019 0.002 PHE C 53 TRP 0.012 0.002 TRP C 479 HIS 0.005 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.25 (17300) covalent geometry : angle 0.71076 / 0.34 (23480) SS BOND : bond 0.00388 / 0.25 ( 37) SS BOND : angle 1.78010 / 1.05 ( 74) hydrogen bonds : bond 0.05160 / 3.36 ( 484) hydrogen bonds : angle 5.08702 / 3.68 ( 1314) link_ALPHA1-2 : bond 0.00740 / 0.37 ( 5) link_ALPHA1-2 : angle 1.94465 / 1.06 ( 15) link_ALPHA1-3 : bond 0.00534 / 0.23 ( 8) link_ALPHA1-3 : angle 1.44157 / 0.87 ( 24) link_ALPHA1-6 : bond 0.00426 / 0.20 ( 8) link_ALPHA1-6 : angle 1.71158 / 1.05 ( 24) link_BETA1-4 : bond 0.00461 / 0.30 ( 30) link_BETA1-4 : angle 1.36308 / 0.93 ( 90) link_NAG-ASN : bond 0.00567 / 0.31 ( 61) link_NAG-ASN : angle 2.72104 / 1.96 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 201 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 523 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8428 (tt) REVERT: B 536 THR cc_start: 0.9090 (t) cc_final: 0.8714 (p) REVERT: C 95 MET cc_start: 0.9035 (ptm) cc_final: 0.7957 (ttp) REVERT: C 292 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8850 (m) REVERT: C 500 ARG cc_start: 0.7590 (ptm160) cc_final: 0.7196 (ptm160) REVERT: F 632 ASP cc_start: 0.8819 (t70) cc_final: 0.8549 (t0) REVERT: G 67 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.7059 (p0) REVERT: G 151 ARG cc_start: 0.8988 (ttm-80) cc_final: 0.8280 (ttm110) REVERT: I 115 SER cc_start: 0.9141 (t) cc_final: 0.8812 (p) REVERT: I 151 ARG cc_start: 0.8508 (tpm170) cc_final: 0.7675 (tpp80) REVERT: I 161 MET cc_start: 0.8423 (mmm) cc_final: 0.7910 (tpp) REVERT: I 205 CYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6503 (m) REVERT: H 72 ASP cc_start: 0.8489 (t0) cc_final: 0.8074 (t0) REVERT: H 94 ARG cc_start: 0.8104 (ttp-170) cc_final: 0.7806 (ttt-90) REVERT: H 100 TYR cc_start: 0.8557 (m-80) cc_final: 0.8115 (m-80) REVERT: L 24 GLN cc_start: 0.7301 (tm-30) cc_final: 0.6915 (mt0) outliers start: 71 outliers final: 49 residues processed: 258 average time/residue: 0.1194 time to fit residues: 45.9896 Evaluate side-chains 242 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 412 ASP Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 178 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 93 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 428 GLN I 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.170846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.140254 restraints weight = 20689.592| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.28 r_work: 0.3457 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17449 Z= 0.130 Angle : 0.683 18.439 23890 Z= 0.312 Chirality : 0.048 0.765 2959 Planarity : 0.004 0.042 2840 Dihedral : 4.674 29.461 2107 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.64 % Allowed : 12.48 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1932 helix: 0.99 (0.28), residues: 387 sheet: 0.19 (0.23), residues: 514 loop : -0.67 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 617 TYR 0.015 0.001 TYR G 486 PHE 0.020 0.001 PHE C 53 TRP 0.012 0.001 TRP C 479 HIS 0.004 0.001 HIS G 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (17300) covalent geometry : angle 0.62137 / 0.30 (23480) SS BOND : bond 0.00319 / 0.21 ( 37) SS BOND : angle 1.48798 / 0.86 ( 74) hydrogen bonds : bond 0.04177 / 2.74 ( 484) hydrogen bonds : angle 4.78001 / 3.47 ( 1314) link_ALPHA1-2 : bond 0.00656 / 0.34 ( 5) link_ALPHA1-2 : angle 1.71182 / 0.95 ( 15) link_ALPHA1-3 : bond 0.00617 / 0.28 ( 8) link_ALPHA1-3 : angle 1.36800 / 0.82 ( 24) link_ALPHA1-6 : bond 0.00489 / 0.21 ( 8) link_ALPHA1-6 : angle 1.52770 / 0.93 ( 24) link_BETA1-4 : bond 0.00414 / 0.27 ( 30) link_BETA1-4 : angle 1.24537 / 0.83 ( 90) link_NAG-ASN : bond 0.00450 / 0.22 ( 61) link_NAG-ASN : angle 2.97204 / 2.02 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 ASN cc_start: 0.7419 (t0) cc_final: 0.7181 (t0) REVERT: B 536 THR cc_start: 0.9102 (t) cc_final: 0.8711 (p) REVERT: C 95 MET cc_start: 0.8957 (ptm) cc_final: 0.7929 (ttp) REVERT: C 292 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8837 (m) REVERT: F 540 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.6471 (mp10) REVERT: G 95 MET cc_start: 0.8335 (ptm) cc_final: 0.7847 (ttp) REVERT: G 151 ARG cc_start: 0.8967 (ttm-80) cc_final: 0.8247 (ttm110) REVERT: I 115 SER cc_start: 0.9097 (t) cc_final: 0.8776 (p) REVERT: I 151 ARG cc_start: 0.8496 (tpm170) cc_final: 0.7604 (tpp80) REVERT: I 161 MET cc_start: 0.8345 (mmm) cc_final: 0.7927 (tpp) REVERT: I 205 CYS cc_start: 0.6682 (OUTLIER) cc_final: 0.6379 (m) REVERT: H 72 ASP cc_start: 0.8481 (t0) cc_final: 0.8068 (t0) REVERT: L 24 GLN cc_start: 0.7228 (tm-30) cc_final: 0.6830 (mt0) outliers start: 63 outliers final: 46 residues processed: 246 average time/residue: 0.1209 time to fit residues: 45.4246 Evaluate side-chains 229 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 35 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 128 optimal weight: 0.3980 chunk 135 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 79 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 103 GLN G 428 GLN I 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.173682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144155 restraints weight = 20717.752| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.19 r_work: 0.3507 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17449 Z= 0.126 Angle : 0.653 18.446 23890 Z= 0.299 Chirality : 0.046 0.533 2959 Planarity : 0.003 0.041 2840 Dihedral : 4.510 28.614 2107 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.47 % Allowed : 12.94 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1932 helix: 1.16 (0.28), residues: 387 sheet: 0.21 (0.22), residues: 559 loop : -0.63 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 500 TYR 0.013 0.001 TYR H 100E PHE 0.017 0.001 PHE C 53 TRP 0.013 0.001 TRP G 96 HIS 0.003 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (17300) covalent geometry : angle 0.59863 / 0.29 (23480) SS BOND : bond 0.00320 / 0.22 ( 37) SS BOND : angle 1.40228 / 0.80 ( 74) hydrogen bonds : bond 0.03868 / 2.53 ( 484) hydrogen bonds : angle 4.67745 / 3.39 ( 1314) link_ALPHA1-2 : bond 0.00671 / 0.34 ( 5) link_ALPHA1-2 : angle 1.66498 / 0.93 ( 15) link_ALPHA1-3 : bond 0.00626 / 0.29 ( 8) link_ALPHA1-3 : angle 1.37009 / 0.82 ( 24) link_ALPHA1-6 : bond 0.00466 / 0.20 ( 8) link_ALPHA1-6 : angle 1.51571 / 0.92 ( 24) link_BETA1-4 : bond 0.00429 / 0.27 ( 30) link_BETA1-4 : angle 1.22595 / 0.82 ( 90) link_NAG-ASN : bond 0.00575 / 0.25 ( 61) link_NAG-ASN : angle 2.72790 / 1.89 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 MET cc_start: 0.8966 (ptm) cc_final: 0.7822 (ttp) REVERT: C 113 ASP cc_start: 0.8625 (m-30) cc_final: 0.8351 (m-30) REVERT: C 292 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8778 (m) REVERT: F 540 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.6914 (mt0) REVERT: F 584 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7715 (mm-30) REVERT: F 626 MET cc_start: 0.8149 (ttt) cc_final: 0.7923 (ttt) REVERT: G 96 TRP cc_start: 0.8454 (m100) cc_final: 0.7886 (m100) REVERT: G 151 ARG cc_start: 0.8987 (ttm-80) cc_final: 0.8300 (ttm110) REVERT: G 217 TYR cc_start: 0.8881 (m-80) cc_final: 0.8598 (m-80) REVERT: I 115 SER cc_start: 0.9147 (t) cc_final: 0.8819 (p) REVERT: I 151 ARG cc_start: 0.8503 (tpm170) cc_final: 0.7596 (tpp80) REVERT: I 161 MET cc_start: 0.8286 (mmm) cc_final: 0.7826 (tpp) REVERT: I 205 CYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6399 (m) REVERT: H 72 ASP cc_start: 0.8459 (t0) cc_final: 0.8054 (t0) REVERT: L 24 GLN cc_start: 0.7254 (tm-30) cc_final: 0.6844 (mt0) outliers start: 60 outliers final: 50 residues processed: 236 average time/residue: 0.1232 time to fit residues: 44.0751 Evaluate side-chains 232 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 60 optimal weight: 0.1980 chunk 176 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 658 GLN G 428 GLN H 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.174367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144839 restraints weight = 20804.493| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.20 r_work: 0.3513 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17449 Z= 0.123 Angle : 0.659 18.421 23890 Z= 0.301 Chirality : 0.048 0.859 2959 Planarity : 0.003 0.040 2840 Dihedral : 4.441 27.457 2107 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.47 % Allowed : 12.71 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 1932 helix: 1.22 (0.28), residues: 387 sheet: 0.27 (0.23), residues: 520 loop : -0.63 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 500 TYR 0.012 0.001 TYR G 173 PHE 0.018 0.001 PHE C 53 TRP 0.015 0.001 TRP C 338 HIS 0.003 0.001 HIS H 100R Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (17300) covalent geometry : angle 0.60652 / 0.29 (23480) SS BOND : bond 0.00288 / 0.19 ( 37) SS BOND : angle 1.32184 / 0.75 ( 74) hydrogen bonds : bond 0.03761 / 2.45 ( 484) hydrogen bonds : angle 4.64004 / 3.36 ( 1314) link_ALPHA1-2 : bond 0.00643 / 0.33 ( 5) link_ALPHA1-2 : angle 1.64990 / 0.92 ( 15) link_ALPHA1-3 : bond 0.00610 / 0.28 ( 8) link_ALPHA1-3 : angle 1.37122 / 0.82 ( 24) link_ALPHA1-6 : bond 0.00461 / 0.20 ( 8) link_ALPHA1-6 : angle 1.50737 / 0.92 ( 24) link_BETA1-4 : bond 0.00426 / 0.27 ( 30) link_BETA1-4 : angle 1.21804 / 0.81 ( 90) link_NAG-ASN : bond 0.00542 / 0.24 ( 61) link_NAG-ASN : angle 2.71285 / 1.91 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 MET cc_start: 0.8979 (ptm) cc_final: 0.7765 (ttp) REVERT: C 113 ASP cc_start: 0.8629 (m-30) cc_final: 0.8371 (m-30) REVERT: C 434 MET cc_start: 0.7814 (tmm) cc_final: 0.7599 (tmm) REVERT: F 540 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.6909 (mt0) REVERT: F 584 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7679 (mm-30) REVERT: G 151 ARG cc_start: 0.8992 (ttm-80) cc_final: 0.8323 (ttm110) REVERT: G 217 TYR cc_start: 0.8824 (m-80) cc_final: 0.8534 (m-80) REVERT: I 115 SER cc_start: 0.9125 (t) cc_final: 0.8809 (p) REVERT: I 151 ARG cc_start: 0.8493 (tpm170) cc_final: 0.7580 (tpp80) REVERT: I 161 MET cc_start: 0.8230 (mmm) cc_final: 0.7777 (tpp) REVERT: I 205 CYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6748 (m) REVERT: H 72 ASP cc_start: 0.8458 (t0) cc_final: 0.8054 (t0) REVERT: H 82 MET cc_start: 0.6954 (mmm) cc_final: 0.6499 (mmm) REVERT: L 24 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6873 (mt0) outliers start: 60 outliers final: 49 residues processed: 234 average time/residue: 0.1160 time to fit residues: 41.1345 Evaluate side-chains 233 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 144 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 133 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 140 optimal weight: 0.0870 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 428 GLN I 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.174634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.145329 restraints weight = 20597.451| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.17 r_work: 0.3521 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17449 Z= 0.124 Angle : 0.650 18.742 23890 Z= 0.297 Chirality : 0.046 0.598 2959 Planarity : 0.003 0.040 2840 Dihedral : 4.372 27.015 2107 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.29 % Allowed : 13.23 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1932 helix: 1.28 (0.28), residues: 387 sheet: 0.26 (0.23), residues: 526 loop : -0.64 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 500 TYR 0.012 0.001 TYR G 173 PHE 0.017 0.001 PHE C 53 TRP 0.012 0.001 TRP C 395 HIS 0.004 0.001 HIS H 100R Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (17300) covalent geometry : angle 0.60058 / 0.29 (23480) SS BOND : bond 0.00280 / 0.19 ( 37) SS BOND : angle 1.27571 / 0.72 ( 74) hydrogen bonds : bond 0.03686 / 2.41 ( 484) hydrogen bonds : angle 4.61789 / 3.34 ( 1314) link_ALPHA1-2 : bond 0.00637 / 0.32 ( 5) link_ALPHA1-2 : angle 1.63809 / 0.92 ( 15) link_ALPHA1-3 : bond 0.00610 / 0.28 ( 8) link_ALPHA1-3 : angle 1.37974 / 0.83 ( 24) link_ALPHA1-6 : bond 0.00446 / 0.20 ( 8) link_ALPHA1-6 : angle 1.50785 / 0.92 ( 24) link_BETA1-4 : bond 0.00421 / 0.27 ( 30) link_BETA1-4 : angle 1.21089 / 0.81 ( 90) link_NAG-ASN : bond 0.00590 / 0.26 ( 61) link_NAG-ASN : angle 2.60536 / 1.87 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 ASP cc_start: 0.8616 (m-30) cc_final: 0.8391 (m-30) REVERT: C 434 MET cc_start: 0.7800 (tmm) cc_final: 0.7579 (tmm) REVERT: F 540 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.6916 (mt0) REVERT: F 584 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7695 (mm-30) REVERT: G 151 ARG cc_start: 0.8989 (ttm-80) cc_final: 0.8305 (ttm110) REVERT: G 217 TYR cc_start: 0.8782 (m-80) cc_final: 0.8488 (m-80) REVERT: I 115 SER cc_start: 0.9116 (t) cc_final: 0.8864 (p) REVERT: I 151 ARG cc_start: 0.8488 (tpm170) cc_final: 0.7612 (tpp80) REVERT: I 161 MET cc_start: 0.8213 (mmm) cc_final: 0.7765 (tpp) REVERT: I 428 GLN cc_start: 0.8496 (mt0) cc_final: 0.8209 (mm-40) REVERT: H 72 ASP cc_start: 0.8443 (t0) cc_final: 0.8010 (t0) outliers start: 57 outliers final: 52 residues processed: 236 average time/residue: 0.1189 time to fit residues: 42.5925 Evaluate side-chains 237 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 294 ILE Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 488 VAL Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 20 optimal weight: 0.0770 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 0.0170 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 656 ASN G 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.174899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145673 restraints weight = 20691.862| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.17 r_work: 0.3521 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17449 Z= 0.122 Angle : 0.643 17.316 23890 Z= 0.295 Chirality : 0.046 0.553 2959 Planarity : 0.003 0.040 2840 Dihedral : 4.343 26.725 2107 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.24 % Allowed : 13.52 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 1932 helix: 1.33 (0.28), residues: 387 sheet: 0.24 (0.22), residues: 565 loop : -0.64 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 500 TYR 0.011 0.001 TYR G 173 PHE 0.017 0.001 PHE C 53 TRP 0.011 0.001 TRP C 96 HIS 0.004 0.001 HIS H 100R Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (17300) covalent geometry : angle 0.59527 / 0.28 (23480) SS BOND : bond 0.00285 / 0.18 ( 37) SS BOND : angle 1.28284 / 0.73 ( 74) hydrogen bonds : bond 0.03609 / 2.36 ( 484) hydrogen bonds : angle 4.60132 / 3.32 ( 1314) link_ALPHA1-2 : bond 0.00623 / 0.32 ( 5) link_ALPHA1-2 : angle 1.62713 / 0.91 ( 15) link_ALPHA1-3 : bond 0.00600 / 0.28 ( 8) link_ALPHA1-3 : angle 1.38188 / 0.83 ( 24) link_ALPHA1-6 : bond 0.00461 / 0.20 ( 8) link_ALPHA1-6 : angle 1.50956 / 0.92 ( 24) link_BETA1-4 : bond 0.00422 / 0.26 ( 30) link_BETA1-4 : angle 1.20396 / 0.80 ( 90) link_NAG-ASN : bond 0.00473 / 0.22 ( 61) link_NAG-ASN : angle 2.51114 / 1.79 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3807.33 seconds wall clock time: 66 minutes 2.08 seconds (3962.08 seconds total)