Starting phenix.real_space_refine on Sun Aug 24 05:04:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fl1_29264/08_2025/8fl1_29264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fl1_29264/08_2025/8fl1_29264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fl1_29264/08_2025/8fl1_29264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fl1_29264/08_2025/8fl1_29264.map" model { file = "/net/cci-nas-00/data/ceres_data/8fl1_29264/08_2025/8fl1_29264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fl1_29264/08_2025/8fl1_29264.cif" } resolution = 3.75 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= 0.004 sd= 0.048 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 10538 2.51 5 N 2808 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16951 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: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3543 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} 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: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3544 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} 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: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1094 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 18 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "I" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 3.93, per 1000 atoms: 0.23 Number of scatterers: 16951 At special positions: 0 Unit cell: (132.126, 129.96, 168.948, 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 3488 8.00 N 2808 7.00 C 10538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " 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=2.03 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=2.04 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=2.04 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 " 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 d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 7 " " MAN e 4 " - " MAN e 5 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 6 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 6 " 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 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 F 703 " - " ASN F 618 " " 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 I 610 " - " ASN I 462 " " 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: 2.09 Conformation dependent library (CDL) restraints added in 752.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 29 sheets defined 23.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 4.530A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 536 through 542' Processing helix chain 'A' and resid 570 through 596 removed outlier: 3.626A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.691A 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 635 removed outlier: 3.647A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 664 removed outlier: 3.508A pdb=" N LEU A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.077A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.556A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.767A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.810A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.927A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.580A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.697A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 4.248A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' 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 352 removed outlier: 3.736A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.390A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 536 through 543' Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.987A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 593 " --> pdb=" O ASP F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.562A pdb=" N ASP F 632 " --> pdb=" O TRP F 628 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.594A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 98 through 116 removed outlier: 4.163A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.575A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.541A 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 Processing helix chain 'G' and resid 474 through 481 removed outlier: 4.174A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 removed outlier: 3.521A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 59 through 64' Processing helix chain 'I' and resid 99 through 115 removed outlier: 3.634A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 3.837A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.613A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 removed outlier: 4.329A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.796A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 28 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: 4.614A 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: 3.528A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP G 35 " --> pdb=" O THR G 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.650A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.932A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.154A 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: 6.700A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 309 " --> pdb=" O GLN C 315 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 322 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: 4.549A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.316A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 55 through 56 removed outlier: 3.611A pdb=" N SER G 56 " --> pdb=" O VAL G 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 91 through 94 removed outlier: 4.081A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.505A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 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 330 through 334 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 330 through 334 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.862A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AB8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.577A pdb=" N LYS I 46 " --> pdb=" O LYS I 490 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'I' and resid 92 through 94 removed outlier: 3.786A pdb=" N PHE I 93 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'I' and resid 130 through 133 removed outlier: 7.024A pdb=" N LYS I 169 " --> pdb=" O TYS H 100H" (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE H 100J" --> pdb=" O LYS I 169 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS I 171 " --> pdb=" O PHE H 100J" (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'I' and resid 202 through 203 removed outlier: 7.178A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC5, 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 298 removed outlier: 3.685A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 329 through 333 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 381 through 385 current: chain 'I' and resid 466 through 470 Processing sheet with id=AC6, first strand: chain 'I' and resid 302 through 312 removed outlier: 6.664A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.752A pdb=" N ARG H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER H 25 " --> pdb=" O ARG H 3 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.045A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'H' and resid 34 through 39 removed outlier: 7.088A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) 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=AD1, 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 46 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 46 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.526A pdb=" N ILE L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE L 75 " --> pdb=" O ILE L 19 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1149 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: 2.70 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5004 1.34 - 1.46: 4416 1.46 - 1.59: 7694 1.59 - 1.71: 1 1.71 - 1.83: 154 Bond restraints: 17269 Sorted by residual: bond pdb=" O3 TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.458 1.635 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.535 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" OH TYS H 100G" pdb=" S TYS H 100G" ideal model delta sigma weight residual 1.679 1.546 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C3 MAN e 4 " pdb=" O3 MAN e 4 " ideal model delta sigma weight residual 1.408 1.474 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CZ TYS H 100G" pdb=" OH TYS H 100G" ideal model delta sigma weight residual 1.371 1.425 -0.054 2.00e-02 2.50e+03 7.28e+00 ... (remaining 17264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 22939 2.20 - 4.40: 414 4.40 - 6.60: 80 6.60 - 8.80: 1 8.80 - 11.00: 3 Bond angle restraints: 23437 Sorted by residual: angle pdb=" CA TYS H 100G" pdb=" C TYS H 100G" pdb=" O TYS H 100G" ideal model delta sigma weight residual 120.80 113.83 6.97 1.70e+00 3.46e-01 1.68e+01 angle pdb=" C CYS I 218 " pdb=" N ALA I 219 " pdb=" CA ALA I 219 " ideal model delta sigma weight residual 120.97 131.74 -10.77 2.84e+00 1.24e-01 1.44e+01 angle pdb=" C2 MAN e 4 " pdb=" C3 MAN e 4 " pdb=" O3 MAN e 4 " ideal model delta sigma weight residual 107.58 118.58 -11.00 3.00e+00 1.11e-01 1.34e+01 angle pdb=" OH TYS H 100H" pdb=" S TYS H 100H" pdb=" O3 TYS H 100H" ideal model delta sigma weight residual 100.21 109.42 -9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" CA GLY G 354 " pdb=" C GLY G 354 " pdb=" O GLY G 354 " ideal model delta sigma weight residual 122.24 119.79 2.45 8.70e-01 1.32e+00 7.91e+00 ... (remaining 23432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.65: 10917 23.65 - 47.30: 663 47.30 - 70.95: 112 70.95 - 94.59: 55 94.59 - 118.24: 27 Dihedral angle restraints: 11774 sinusoidal: 6094 harmonic: 5680 Sorted by residual: dihedral pdb=" CB CYS A 605 " pdb=" SG CYS A 605 " pdb=" SG CYS C 501 " pdb=" CB CYS C 501 " ideal model delta sinusoidal sigma weight residual -86.00 -150.38 64.38 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -150.22 64.22 1 1.00e+01 1.00e-02 5.43e+01 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 -146.05 60.05 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 11771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2480 0.061 - 0.123: 420 0.123 - 0.184: 32 0.184 - 0.246: 0 0.246 - 0.307: 9 Chirality restraints: 2941 Sorted by residual: chirality pdb=" C1 NAG G 608 " pdb=" ND2 ASN G 355 " pdb=" C2 NAG G 608 " pdb=" O5 NAG G 608 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3 MAN e 4 " pdb=" C2 MAN e 4 " pdb=" C4 MAN e 4 " pdb=" O3 MAN e 4 " both_signs ideal model delta sigma weight residual False 2.47 2.17 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2938 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 3 " -0.109 9.50e-02 1.11e+02 4.88e-02 1.47e+00 pdb=" NE ARG H 3 " 0.007 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 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 448 " 0.011 2.00e-02 2.50e+03 9.82e-03 1.21e+00 pdb=" CG ASN C 448 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN C 448 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 448 " -0.011 2.00e-02 2.50e+03 pdb=" C1 NAG C 610 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 75 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO I 76 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO I 76 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 76 " 0.015 5.00e-02 4.00e+02 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3537 2.79 - 3.32: 15367 3.32 - 3.84: 25820 3.84 - 4.37: 30107 4.37 - 4.90: 52026 Nonbonded interactions: 126857 Sorted by model distance: nonbonded pdb=" OD1 ASN C 137 " pdb=" N2 NAG C 611 " model vdw 2.259 3.120 nonbonded pdb=" NH1 ARG G 298 " pdb=" OD1 ASN G 302 " model vdw 2.273 3.120 nonbonded pdb=" OG1 THR G 163 " pdb=" OE1 GLU G 164 " model vdw 2.274 3.040 nonbonded pdb=" OG SER L 14 " pdb=" OE1 GLN L 17 " model vdw 2.278 3.040 nonbonded pdb=" O LEU L 4 " pdb=" OG1 THR L 100 " model vdw 2.280 3.040 ... (remaining 126852 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 610) selection = (chain 'G' and (resid 33 through 185 or resid 189 through 610)) selection = (chain 'I' and resid 33 through 610) } 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 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'J' and (resid 1 or resid 4 through 6)) selection = (chain 'X' and (resid 1 or resid 4 through 6)) selection = (chain 'e' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'Q' selection = chain 'V' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.070 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 0.177 17415 Z= 0.249 Angle : 0.702 10.997 23837 Z= 0.297 Chirality : 0.048 0.307 2941 Planarity : 0.003 0.049 2846 Dihedral : 16.101 118.243 7992 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.19), residues: 1934 helix: 0.41 (0.28), residues: 362 sheet: 1.01 (0.24), residues: 490 loop : -0.31 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 588 TYR 0.008 0.001 TYR L 49 PHE 0.010 0.001 PHE C 223 TRP 0.006 0.001 TRP H 103 HIS 0.003 0.000 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00500 (17269) covalent geometry : angle 0.67685 (23437) SS BOND : bond 0.00266 ( 38) SS BOND : angle 1.37668 ( 76) hydrogen bonds : bond 0.28822 ( 408) hydrogen bonds : angle 8.50327 ( 1149) link_ALPHA1-2 : bond 0.00714 ( 3) link_ALPHA1-2 : angle 1.59062 ( 9) link_ALPHA1-3 : bond 0.00622 ( 7) link_ALPHA1-3 : angle 2.75689 ( 21) link_ALPHA1-6 : bond 0.00400 ( 6) link_ALPHA1-6 : angle 1.45372 ( 18) link_BETA1-4 : bond 0.00467 ( 29) link_BETA1-4 : angle 1.13501 ( 87) link_NAG-ASN : bond 0.00364 ( 63) link_NAG-ASN : angle 1.67990 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.628 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: A 655 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7469 (ptmm) REVERT: B 579 ARG cc_start: 0.8932 (ttm-80) cc_final: 0.8674 (ttm170) REVERT: B 612 SER cc_start: 0.8931 (m) cc_final: 0.8405 (p) REVERT: B 615 SER cc_start: 0.8688 (t) cc_final: 0.8361 (m) REVERT: C 128 THR cc_start: 0.8773 (m) cc_final: 0.8484 (p) REVERT: G 97 LYS cc_start: 0.7919 (mttp) cc_final: 0.7624 (mttp) REVERT: G 246 GLN cc_start: 0.6151 (mp10) cc_final: 0.5516 (mp10) REVERT: G 277 ILE cc_start: 0.8144 (mm) cc_final: 0.7880 (mm) REVERT: I 121 LYS cc_start: 0.8141 (mttp) cc_final: 0.7899 (tttm) REVERT: I 474 ASP cc_start: 0.6285 (t0) cc_final: 0.6079 (t0) REVERT: H 34 MET cc_start: 0.6912 (mmt) cc_final: 0.6343 (mmt) REVERT: H 52 LYS cc_start: 0.7686 (mtpt) cc_final: 0.6705 (mtpp) REVERT: H 70 SER cc_start: 0.8258 (t) cc_final: 0.7944 (p) REVERT: H 100 ASP cc_start: 0.8659 (t0) cc_final: 0.8450 (t70) REVERT: H 100 MET cc_start: 0.8044 (mtt) cc_final: 0.7686 (mtp) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.1355 time to fit residues: 81.2008 Evaluate side-chains 231 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN C 85 HIS C 195 ASN C 249 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN G 188 ASN G 249 HIS ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN L 17 GLN L 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.151792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118754 restraints weight = 25473.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120112 restraints weight = 20828.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.121716 restraints weight = 17522.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122242 restraints weight = 14888.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122504 restraints weight = 14216.140| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 17415 Z= 0.291 Angle : 0.842 17.849 23837 Z= 0.393 Chirality : 0.052 0.393 2941 Planarity : 0.005 0.041 2846 Dihedral : 12.366 110.824 4331 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.58 % Allowed : 10.50 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.19), residues: 1934 helix: 0.15 (0.26), residues: 373 sheet: 0.30 (0.23), residues: 529 loop : -0.41 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 503 TYR 0.021 0.002 TYR F 638 PHE 0.035 0.003 PHE C 382 TRP 0.023 0.002 TRP I 479 HIS 0.008 0.002 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00685 (17269) covalent geometry : angle 0.76959 (23437) SS BOND : bond 0.00582 ( 38) SS BOND : angle 1.67213 ( 76) hydrogen bonds : bond 0.07284 ( 408) hydrogen bonds : angle 5.93712 ( 1149) link_ALPHA1-2 : bond 0.01045 ( 3) link_ALPHA1-2 : angle 2.21629 ( 9) link_ALPHA1-3 : bond 0.01223 ( 7) link_ALPHA1-3 : angle 3.96064 ( 21) link_ALPHA1-6 : bond 0.00474 ( 6) link_ALPHA1-6 : angle 2.04627 ( 18) link_BETA1-4 : bond 0.00456 ( 29) link_BETA1-4 : angle 1.45741 ( 87) link_NAG-ASN : bond 0.00637 ( 63) link_NAG-ASN : angle 3.37613 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 239 time to evaluate : 0.535 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: A 581 LEU cc_start: 0.8695 (tp) cc_final: 0.8474 (tp) REVERT: A 655 LYS cc_start: 0.7953 (mmmt) cc_final: 0.7685 (ptmm) REVERT: B 607 ASN cc_start: 0.7983 (p0) cc_final: 0.7583 (p0) REVERT: B 615 SER cc_start: 0.8788 (t) cc_final: 0.8482 (m) REVERT: B 616 ASN cc_start: 0.8272 (p0) cc_final: 0.7987 (p0) REVERT: B 655 LYS cc_start: 0.8058 (ptpt) cc_final: 0.7757 (pptt) REVERT: C 434 MET cc_start: 0.7689 (tmm) cc_final: 0.7255 (tmm) REVERT: F 590 GLN cc_start: 0.9215 (tp40) cc_final: 0.8891 (tp40) REVERT: F 626 MET cc_start: 0.7260 (ttm) cc_final: 0.7030 (ttm) REVERT: G 97 LYS cc_start: 0.8226 (mttp) cc_final: 0.7802 (mttp) REVERT: G 188 ASN cc_start: 0.6485 (OUTLIER) cc_final: 0.6241 (t0) REVERT: I 104 MET cc_start: 0.8532 (ttt) cc_final: 0.8304 (ttt) REVERT: I 121 LYS cc_start: 0.8307 (mttp) cc_final: 0.7997 (tttm) REVERT: I 340 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7318 (tm-30) REVERT: H 32 GLN cc_start: 0.7186 (mt0) cc_final: 0.6972 (mt0) REVERT: H 52 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8208 (mtmt) REVERT: H 56 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8080 (pp20) REVERT: H 89 THR cc_start: 0.7389 (t) cc_final: 0.7049 (t) REVERT: H 100 ASP cc_start: 0.8697 (t0) cc_final: 0.8450 (t0) REVERT: L 50 ASP cc_start: 0.7536 (t0) cc_final: 0.7185 (t0) outliers start: 62 outliers final: 45 residues processed: 273 average time/residue: 0.1282 time to fit residues: 52.2360 Evaluate side-chains 253 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 132 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 177 optimal weight: 0.0000 chunk 28 optimal weight: 6.9990 chunk 90 optimal weight: 0.0870 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN C 67 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 ASN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95AHIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.161709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.130576 restraints weight = 25156.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133295 restraints weight = 18924.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135428 restraints weight = 15159.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135762 restraints weight = 12939.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135907 restraints weight = 12287.297| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 17415 Z= 0.131 Angle : 0.751 29.960 23837 Z= 0.332 Chirality : 0.048 0.550 2941 Planarity : 0.003 0.041 2846 Dihedral : 11.181 102.683 4331 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.77 % Allowed : 13.91 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.19), residues: 1934 helix: 0.63 (0.27), residues: 375 sheet: 0.40 (0.23), residues: 518 loop : -0.31 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 166 TYR 0.019 0.001 TYR B 638 PHE 0.020 0.001 PHE C 382 TRP 0.024 0.001 TRP L 35 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00284 (17269) covalent geometry : angle 0.62532 (23437) SS BOND : bond 0.00427 ( 38) SS BOND : angle 1.70810 ( 76) hydrogen bonds : bond 0.05752 ( 408) hydrogen bonds : angle 5.26595 ( 1149) link_ALPHA1-2 : bond 0.00724 ( 3) link_ALPHA1-2 : angle 1.68794 ( 9) link_ALPHA1-3 : bond 0.01230 ( 7) link_ALPHA1-3 : angle 3.22711 ( 21) link_ALPHA1-6 : bond 0.00670 ( 6) link_ALPHA1-6 : angle 1.71998 ( 18) link_BETA1-4 : bond 0.00419 ( 29) link_BETA1-4 : angle 1.24129 ( 87) link_NAG-ASN : bond 0.00708 ( 63) link_NAG-ASN : angle 4.39003 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 607 ASN cc_start: 0.7800 (p0) cc_final: 0.7451 (p0) REVERT: B 615 SER cc_start: 0.8782 (t) cc_final: 0.8506 (m) REVERT: B 655 LYS cc_start: 0.8010 (ptpt) cc_final: 0.7759 (pptt) REVERT: C 104 MET cc_start: 0.8346 (ttm) cc_final: 0.8120 (ttt) REVERT: C 190 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: C 337 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8309 (m) REVERT: F 590 GLN cc_start: 0.9140 (tp40) cc_final: 0.8872 (tp40) REVERT: G 97 LYS cc_start: 0.8223 (mttp) cc_final: 0.7803 (mttp) REVERT: I 121 LYS cc_start: 0.8293 (mttp) cc_final: 0.8071 (tttm) REVERT: H 52 LYS cc_start: 0.8372 (mtpt) cc_final: 0.8095 (mtmt) REVERT: H 56 GLU cc_start: 0.8190 (pm20) cc_final: 0.7895 (pp20) REVERT: H 100 ASP cc_start: 0.8630 (t0) cc_final: 0.8404 (t0) outliers start: 48 outliers final: 32 residues processed: 249 average time/residue: 0.1297 time to fit residues: 48.9314 Evaluate side-chains 229 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 86 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN B 653 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN G 188 ASN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN ** L 95AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.157423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125756 restraints weight = 25077.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128154 restraints weight = 19446.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.129992 restraints weight = 16396.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.130324 restraints weight = 13598.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131974 restraints weight = 13356.293| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17415 Z= 0.187 Angle : 0.746 23.341 23837 Z= 0.338 Chirality : 0.048 0.465 2941 Planarity : 0.004 0.074 2846 Dihedral : 10.061 99.217 4331 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.92 % Allowed : 14.14 % Favored : 81.94 % 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 aren not related in a simple way. whole: -0.08 (0.19), residues: 1934 helix: 0.63 (0.27), residues: 377 sheet: 0.20 (0.23), residues: 490 loop : -0.35 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 38 TYR 0.021 0.002 TYR B 638 PHE 0.017 0.002 PHE C 382 TRP 0.030 0.002 TRP L 35 HIS 0.005 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00437 (17269) covalent geometry : angle 0.65281 (23437) SS BOND : bond 0.00409 ( 38) SS BOND : angle 1.93795 ( 76) hydrogen bonds : bond 0.05239 ( 408) hydrogen bonds : angle 5.06845 ( 1149) link_ALPHA1-2 : bond 0.00592 ( 3) link_ALPHA1-2 : angle 1.80750 ( 9) link_ALPHA1-3 : bond 0.01201 ( 7) link_ALPHA1-3 : angle 3.29333 ( 21) link_ALPHA1-6 : bond 0.00747 ( 6) link_ALPHA1-6 : angle 1.52320 ( 18) link_BETA1-4 : bond 0.00455 ( 29) link_BETA1-4 : angle 1.28653 ( 87) link_NAG-ASN : bond 0.00611 ( 63) link_NAG-ASN : angle 3.68501 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 217 time to evaluate : 0.662 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: B 615 SER cc_start: 0.8951 (t) cc_final: 0.8688 (m) REVERT: C 337 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8502 (m) REVERT: G 97 LYS cc_start: 0.8373 (mttp) cc_final: 0.7883 (mttp) REVERT: H 52 LYS cc_start: 0.8482 (mtpt) cc_final: 0.7855 (mtpt) REVERT: H 100 ASP cc_start: 0.8610 (t0) cc_final: 0.8407 (t0) outliers start: 68 outliers final: 52 residues processed: 263 average time/residue: 0.1313 time to fit residues: 52.6173 Evaluate side-chains 244 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain L residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 9 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 101 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN C 258 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** L 95AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.163949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129682 restraints weight = 25444.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133480 restraints weight = 19558.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134895 restraints weight = 15385.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134968 restraints weight = 13619.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135260 restraints weight = 12922.812| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17415 Z= 0.131 Angle : 0.694 20.815 23837 Z= 0.314 Chirality : 0.047 0.481 2941 Planarity : 0.003 0.042 2846 Dihedral : 9.359 96.134 4331 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.58 % Allowed : 16.21 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.19), residues: 1934 helix: 0.86 (0.28), residues: 376 sheet: 0.31 (0.23), residues: 492 loop : -0.33 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 166 TYR 0.022 0.001 TYR A 638 PHE 0.018 0.001 PHE C 382 TRP 0.029 0.001 TRP L 35 HIS 0.005 0.001 HIS L 95A Details of bonding type rmsd covalent geometry : bond 0.00299 (17269) covalent geometry : angle 0.60580 (23437) SS BOND : bond 0.00342 ( 38) SS BOND : angle 1.62482 ( 76) hydrogen bonds : bond 0.04641 ( 408) hydrogen bonds : angle 4.86562 ( 1149) link_ALPHA1-2 : bond 0.00567 ( 3) link_ALPHA1-2 : angle 1.78330 ( 9) link_ALPHA1-3 : bond 0.01238 ( 7) link_ALPHA1-3 : angle 3.19619 ( 21) link_ALPHA1-6 : bond 0.00810 ( 6) link_ALPHA1-6 : angle 1.39741 ( 18) link_BETA1-4 : bond 0.00426 ( 29) link_BETA1-4 : angle 1.20944 ( 87) link_NAG-ASN : bond 0.00555 ( 63) link_NAG-ASN : angle 3.48051 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 SER cc_start: 0.8945 (t) cc_final: 0.8686 (m) REVERT: B 655 LYS cc_start: 0.8150 (ptpt) cc_final: 0.7770 (pptt) REVERT: C 190 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: C 337 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8416 (m) REVERT: G 97 LYS cc_start: 0.8214 (mttp) cc_final: 0.7798 (mttp) REVERT: G 215 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8248 (tp) REVERT: I 112 TRP cc_start: 0.8585 (t-100) cc_final: 0.8323 (t-100) REVERT: H 46 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8239 (mm-30) REVERT: H 52 LYS cc_start: 0.8441 (mtpt) cc_final: 0.7789 (mtpt) REVERT: H 100 ASP cc_start: 0.8629 (t0) cc_final: 0.8425 (t0) outliers start: 62 outliers final: 45 residues processed: 249 average time/residue: 0.1306 time to fit residues: 50.3292 Evaluate side-chains 241 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain L residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 189 optimal weight: 0.0060 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 653 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.162736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127954 restraints weight = 25449.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.132369 restraints weight = 19580.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133415 restraints weight = 15443.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134126 restraints weight = 13197.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134206 restraints weight = 12992.833| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17415 Z= 0.156 Angle : 0.697 18.489 23837 Z= 0.316 Chirality : 0.047 0.463 2941 Planarity : 0.003 0.042 2846 Dihedral : 8.805 101.279 4331 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.98 % Allowed : 16.45 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.19), residues: 1934 helix: 0.83 (0.28), residues: 383 sheet: 0.26 (0.23), residues: 488 loop : -0.34 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.016 0.001 TYR A 638 PHE 0.016 0.001 PHE C 382 TRP 0.028 0.001 TRP L 35 HIS 0.006 0.001 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00363 (17269) covalent geometry : angle 0.61807 (23437) SS BOND : bond 0.00384 ( 38) SS BOND : angle 1.69353 ( 76) hydrogen bonds : bond 0.04466 ( 408) hydrogen bonds : angle 4.80654 ( 1149) link_ALPHA1-2 : bond 0.00514 ( 3) link_ALPHA1-2 : angle 1.85636 ( 9) link_ALPHA1-3 : bond 0.01189 ( 7) link_ALPHA1-3 : angle 3.17029 ( 21) link_ALPHA1-6 : bond 0.00727 ( 6) link_ALPHA1-6 : angle 1.48820 ( 18) link_BETA1-4 : bond 0.00448 ( 29) link_BETA1-4 : angle 1.21845 ( 87) link_NAG-ASN : bond 0.00559 ( 63) link_NAG-ASN : angle 3.24314 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 206 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 SER cc_start: 0.8923 (t) cc_final: 0.8595 (m) REVERT: C 190 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: C 337 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8421 (m) REVERT: F 542 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7575 (ttm110) REVERT: G 97 LYS cc_start: 0.8266 (mttp) cc_final: 0.7832 (mttp) REVERT: G 102 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: G 215 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8299 (tp) REVERT: I 112 TRP cc_start: 0.8562 (t-100) cc_final: 0.8266 (t-100) REVERT: H 52 LYS cc_start: 0.8397 (mtpt) cc_final: 0.7941 (mtpt) REVERT: H 100 ASP cc_start: 0.8598 (t0) cc_final: 0.8396 (t0) outliers start: 69 outliers final: 48 residues processed: 255 average time/residue: 0.1357 time to fit residues: 52.4879 Evaluate side-chains 242 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 140 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS ** L 95AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.160263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127616 restraints weight = 24969.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131514 restraints weight = 19679.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133643 restraints weight = 15044.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133365 restraints weight = 12564.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133954 restraints weight = 12356.388| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17415 Z= 0.122 Angle : 0.704 18.199 23837 Z= 0.315 Chirality : 0.047 0.478 2941 Planarity : 0.003 0.041 2846 Dihedral : 8.306 104.042 4331 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.23 % Allowed : 17.71 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.19), residues: 1934 helix: 0.98 (0.28), residues: 383 sheet: 0.35 (0.23), residues: 485 loop : -0.29 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 166 TYR 0.032 0.001 TYR H 58 PHE 0.016 0.001 PHE C 382 TRP 0.030 0.001 TRP L 35 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00275 (17269) covalent geometry : angle 0.61575 (23437) SS BOND : bond 0.00535 ( 38) SS BOND : angle 1.61572 ( 76) hydrogen bonds : bond 0.04065 ( 408) hydrogen bonds : angle 4.66884 ( 1149) link_ALPHA1-2 : bond 0.00492 ( 3) link_ALPHA1-2 : angle 1.82873 ( 9) link_ALPHA1-3 : bond 0.01190 ( 7) link_ALPHA1-3 : angle 3.02242 ( 21) link_ALPHA1-6 : bond 0.00752 ( 6) link_ALPHA1-6 : angle 1.47627 ( 18) link_BETA1-4 : bond 0.00435 ( 29) link_BETA1-4 : angle 1.19621 ( 87) link_NAG-ASN : bond 0.00565 ( 63) link_NAG-ASN : angle 3.52876 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6741 (p0) REVERT: B 615 SER cc_start: 0.8932 (t) cc_final: 0.8664 (m) REVERT: C 104 MET cc_start: 0.8493 (ttm) cc_final: 0.8170 (ttt) REVERT: C 190 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: C 337 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8356 (m) REVERT: F 542 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7545 (ttm110) REVERT: G 97 LYS cc_start: 0.8250 (mttp) cc_final: 0.7819 (mttp) REVERT: G 102 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: G 215 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8286 (tp) REVERT: I 112 TRP cc_start: 0.8542 (t-100) cc_final: 0.8268 (t-100) REVERT: H 52 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8045 (mtpt) outliers start: 56 outliers final: 42 residues processed: 234 average time/residue: 0.1341 time to fit residues: 47.8043 Evaluate side-chains 226 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 165 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.158541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126461 restraints weight = 25383.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128640 restraints weight = 19736.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.130207 restraints weight = 17036.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131227 restraints weight = 13921.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131474 restraints weight = 13174.741| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17415 Z= 0.153 Angle : 0.712 16.100 23837 Z= 0.323 Chirality : 0.047 0.488 2941 Planarity : 0.003 0.041 2846 Dihedral : 7.909 107.578 4331 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.35 % Allowed : 18.00 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.19), residues: 1934 helix: 0.96 (0.28), residues: 382 sheet: 0.34 (0.24), residues: 476 loop : -0.35 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 503 TYR 0.022 0.001 TYR H 58 PHE 0.015 0.001 PHE C 382 TRP 0.023 0.001 TRP F 631 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00358 (17269) covalent geometry : angle 0.62864 (23437) SS BOND : bond 0.00389 ( 38) SS BOND : angle 1.64190 ( 76) hydrogen bonds : bond 0.04230 ( 408) hydrogen bonds : angle 4.70346 ( 1149) link_ALPHA1-2 : bond 0.00499 ( 3) link_ALPHA1-2 : angle 1.86508 ( 9) link_ALPHA1-3 : bond 0.01340 ( 7) link_ALPHA1-3 : angle 2.14773 ( 21) link_ALPHA1-6 : bond 0.00732 ( 6) link_ALPHA1-6 : angle 1.63530 ( 18) link_BETA1-4 : bond 0.00424 ( 29) link_BETA1-4 : angle 1.23059 ( 87) link_NAG-ASN : bond 0.00540 ( 63) link_NAG-ASN : angle 3.50167 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 191 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.6802 (p0) REVERT: B 612 SER cc_start: 0.8665 (m) cc_final: 0.8332 (p) REVERT: B 615 SER cc_start: 0.8951 (t) cc_final: 0.8679 (m) REVERT: B 655 LYS cc_start: 0.8286 (ptpt) cc_final: 0.7864 (pptt) REVERT: C 104 MET cc_start: 0.8546 (ttm) cc_final: 0.8164 (ttt) REVERT: C 190 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: F 542 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7594 (ttm110) REVERT: G 97 LYS cc_start: 0.8297 (mttp) cc_final: 0.7849 (mttp) REVERT: G 102 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: G 215 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8290 (tp) REVERT: H 52 LYS cc_start: 0.8374 (mtpt) cc_final: 0.8072 (mtpt) outliers start: 58 outliers final: 45 residues processed: 231 average time/residue: 0.1241 time to fit residues: 44.3185 Evaluate side-chains 229 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.159131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127399 restraints weight = 25221.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.129718 restraints weight = 19689.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131455 restraints weight = 16423.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131785 restraints weight = 13890.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132272 restraints weight = 13353.252| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17415 Z= 0.138 Angle : 0.696 15.156 23837 Z= 0.316 Chirality : 0.047 0.485 2941 Planarity : 0.003 0.041 2846 Dihedral : 7.765 109.226 4331 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.23 % Allowed : 18.41 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.19), residues: 1934 helix: 1.02 (0.28), residues: 382 sheet: 0.33 (0.24), residues: 476 loop : -0.33 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 503 TYR 0.028 0.001 TYR A 638 PHE 0.016 0.001 PHE C 382 TRP 0.021 0.001 TRP L 35 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00324 (17269) covalent geometry : angle 0.62115 (23437) SS BOND : bond 0.00382 ( 38) SS BOND : angle 1.61499 ( 76) hydrogen bonds : bond 0.04074 ( 408) hydrogen bonds : angle 4.67258 ( 1149) link_ALPHA1-2 : bond 0.00499 ( 3) link_ALPHA1-2 : angle 1.85159 ( 9) link_ALPHA1-3 : bond 0.01039 ( 7) link_ALPHA1-3 : angle 1.90743 ( 21) link_ALPHA1-6 : bond 0.00702 ( 6) link_ALPHA1-6 : angle 1.48787 ( 18) link_BETA1-4 : bond 0.00434 ( 29) link_BETA1-4 : angle 1.20321 ( 87) link_NAG-ASN : bond 0.00518 ( 63) link_NAG-ASN : angle 3.27874 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6773 (p0) REVERT: B 612 SER cc_start: 0.8675 (m) cc_final: 0.8341 (p) REVERT: B 615 SER cc_start: 0.8951 (t) cc_final: 0.8677 (m) REVERT: B 655 LYS cc_start: 0.8293 (ptpt) cc_final: 0.7824 (pptt) REVERT: C 104 MET cc_start: 0.8527 (ttm) cc_final: 0.8201 (ttt) REVERT: C 190 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: C 334 SER cc_start: 0.8497 (t) cc_final: 0.8292 (p) REVERT: F 542 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7615 (ttm110) REVERT: G 97 LYS cc_start: 0.8318 (mttp) cc_final: 0.7885 (mttp) REVERT: G 102 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6286 (mp0) REVERT: G 215 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8093 (tp) REVERT: H 52 LYS cc_start: 0.8393 (mtpt) cc_final: 0.8123 (mtpt) REVERT: H 79 TYR cc_start: 0.7918 (m-10) cc_final: 0.7647 (m-10) outliers start: 56 outliers final: 48 residues processed: 227 average time/residue: 0.1402 time to fit residues: 48.4075 Evaluate side-chains 227 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 175 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 176 optimal weight: 0.5980 chunk 179 optimal weight: 4.9990 chunk 132 optimal weight: 0.0270 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.162441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128571 restraints weight = 25538.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131178 restraints weight = 19954.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133325 restraints weight = 16878.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133302 restraints weight = 14076.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.133617 restraints weight = 13443.172| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17415 Z= 0.145 Angle : 0.705 17.039 23837 Z= 0.322 Chirality : 0.047 0.473 2941 Planarity : 0.003 0.041 2846 Dihedral : 7.677 111.317 4331 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.00 % Allowed : 18.93 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 1934 helix: 1.04 (0.28), residues: 384 sheet: 0.33 (0.24), residues: 484 loop : -0.38 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.020 0.001 TYR A 638 PHE 0.016 0.001 PHE C 382 TRP 0.035 0.001 TRP C 35 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00341 (17269) covalent geometry : angle 0.62595 (23437) SS BOND : bond 0.00382 ( 38) SS BOND : angle 1.61356 ( 76) hydrogen bonds : bond 0.04071 ( 408) hydrogen bonds : angle 4.67026 ( 1149) link_ALPHA1-2 : bond 0.00437 ( 3) link_ALPHA1-2 : angle 1.84652 ( 9) link_ALPHA1-3 : bond 0.00980 ( 7) link_ALPHA1-3 : angle 1.94096 ( 21) link_ALPHA1-6 : bond 0.00706 ( 6) link_ALPHA1-6 : angle 1.54952 ( 18) link_BETA1-4 : bond 0.00440 ( 29) link_BETA1-4 : angle 1.21299 ( 87) link_NAG-ASN : bond 0.00506 ( 63) link_NAG-ASN : angle 3.39192 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7300 (m-30) cc_final: 0.6658 (p0) REVERT: B 612 SER cc_start: 0.8675 (m) cc_final: 0.8319 (p) REVERT: B 615 SER cc_start: 0.8960 (t) cc_final: 0.8650 (m) REVERT: B 655 LYS cc_start: 0.8340 (ptpt) cc_final: 0.7817 (pptt) REVERT: C 104 MET cc_start: 0.8585 (ttm) cc_final: 0.8217 (ttt) REVERT: C 190 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: C 334 SER cc_start: 0.8578 (t) cc_final: 0.8274 (p) REVERT: F 542 ARG cc_start: 0.7911 (mtp85) cc_final: 0.7611 (ttm110) REVERT: G 97 LYS cc_start: 0.8325 (mttp) cc_final: 0.7866 (mttp) REVERT: G 102 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: G 215 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8041 (tp) REVERT: H 79 TYR cc_start: 0.7948 (m-10) cc_final: 0.7681 (m-10) outliers start: 52 outliers final: 47 residues processed: 214 average time/residue: 0.1391 time to fit residues: 45.4972 Evaluate side-chains 221 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 49 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129214 restraints weight = 25467.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134856 restraints weight = 19084.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.135179 restraints weight = 14464.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.135353 restraints weight = 12375.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135536 restraints weight = 12322.691| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17415 Z= 0.126 Angle : 0.692 16.598 23837 Z= 0.315 Chirality : 0.047 0.468 2941 Planarity : 0.003 0.041 2846 Dihedral : 7.584 112.038 4331 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.00 % Allowed : 19.04 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.19), residues: 1934 helix: 1.13 (0.28), residues: 384 sheet: 0.38 (0.24), residues: 494 loop : -0.38 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 166 TYR 0.018 0.001 TYR H 58 PHE 0.016 0.001 PHE C 382 TRP 0.038 0.002 TRP H 36 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00293 (17269) covalent geometry : angle 0.61560 (23437) SS BOND : bond 0.00379 ( 38) SS BOND : angle 1.60278 ( 76) hydrogen bonds : bond 0.03884 ( 408) hydrogen bonds : angle 4.58947 ( 1149) link_ALPHA1-2 : bond 0.00484 ( 3) link_ALPHA1-2 : angle 1.82284 ( 9) link_ALPHA1-3 : bond 0.00948 ( 7) link_ALPHA1-3 : angle 1.82834 ( 21) link_ALPHA1-6 : bond 0.00697 ( 6) link_ALPHA1-6 : angle 1.49427 ( 18) link_BETA1-4 : bond 0.00434 ( 29) link_BETA1-4 : angle 1.19465 ( 87) link_NAG-ASN : bond 0.00490 ( 63) link_NAG-ASN : angle 3.30503 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.56 seconds wall clock time: 46 minutes 40.67 seconds (2800.67 seconds total)