Starting phenix.real_space_refine on Sun May 18 15:38:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fl1_29264/05_2025/8fl1_29264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fl1_29264/05_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_29264/05_2025/8fl1_29264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fl1_29264/05_2025/8fl1_29264.map" model { file = "/net/cci-nas-00/data/ceres_data/8fl1_29264/05_2025/8fl1_29264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fl1_29264/05_2025/8fl1_29264.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.41, per 1000 atoms: 0.61 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: 5.11 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.00 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: 4.90 Time building geometry restraints manager: 5.85 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 664 or resid 701 through 702)) selection = chain 'B' selection = (chain 'F' and (resid 519 through 546 or resid 569 through 664 or resid 701 thro \ ugh 702)) } ncs_group { reference = (chain 'C' and (resid 33 through 505 or resid 601 through 610)) selection = (chain 'G' and (resid 33 through 185 or resid 189 through 505 or resid 601 throu \ gh 610)) selection = (chain 'I' and (resid 33 through 505 or resid 601 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 38.790 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP H 103 HIS 0.003 0.000 HIS I 374 PHE 0.010 0.001 PHE C 223 TYR 0.008 0.001 TYR L 49 ARG 0.008 0.000 ARG A 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 63) link_NAG-ASN : angle 1.67990 ( 189) 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_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) hydrogen bonds : bond 0.28822 ( 408) hydrogen bonds : angle 8.50327 ( 1149) SS BOND : bond 0.00266 ( 38) SS BOND : angle 1.37668 ( 76) covalent geometry : bond 0.00500 (17269) covalent geometry : angle 0.67685 (23437) *********************** 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 : 1.921 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: 0.2957 time to fit residues: 176.9846 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 : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.9990 chunk 147 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 99 optimal weight: 0.0770 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 176 optimal weight: 4.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 195 ASN C 249 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN G 249 HIS ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN L 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128667 restraints weight = 25147.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132034 restraints weight = 17216.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134266 restraints weight = 13570.902| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17415 Z= 0.141 Angle : 0.710 17.799 23837 Z= 0.324 Chirality : 0.048 0.392 2941 Planarity : 0.004 0.041 2846 Dihedral : 12.324 110.129 4331 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.31 % Allowed : 9.23 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1934 helix: 0.44 (0.27), residues: 371 sheet: 0.63 (0.23), residues: 529 loop : -0.27 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 35 HIS 0.004 0.001 HIS G 105 PHE 0.028 0.001 PHE C 382 TYR 0.017 0.001 TYR L 36 ARG 0.006 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 63) link_NAG-ASN : angle 3.22966 ( 189) link_ALPHA1-6 : bond 0.00571 ( 6) link_ALPHA1-6 : angle 1.87397 ( 18) link_BETA1-4 : bond 0.00461 ( 29) link_BETA1-4 : angle 1.34544 ( 87) link_ALPHA1-2 : bond 0.00982 ( 3) link_ALPHA1-2 : angle 1.76349 ( 9) link_ALPHA1-3 : bond 0.01178 ( 7) link_ALPHA1-3 : angle 3.71576 ( 21) hydrogen bonds : bond 0.07103 ( 408) hydrogen bonds : angle 5.88938 ( 1149) SS BOND : bond 0.00302 ( 38) SS BOND : angle 1.12545 ( 76) covalent geometry : bond 0.00295 (17269) covalent geometry : angle 0.63330 (23437) *********************** 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 291 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 607 ASN cc_start: 0.7567 (p0) cc_final: 0.7142 (p0) REVERT: B 612 SER cc_start: 0.8356 (m) cc_final: 0.8118 (p) REVERT: B 615 SER cc_start: 0.8709 (t) cc_final: 0.8398 (m) REVERT: B 655 LYS cc_start: 0.7906 (ptpt) cc_final: 0.7610 (pptt) REVERT: C 434 MET cc_start: 0.7423 (tmm) cc_final: 0.7003 (tmm) REVERT: F 590 GLN cc_start: 0.9100 (tp40) cc_final: 0.8773 (tp40) REVERT: F 626 MET cc_start: 0.7035 (ttm) cc_final: 0.6803 (ttm) REVERT: G 97 LYS cc_start: 0.8154 (mttp) cc_final: 0.7810 (mttp) REVERT: G 475 MET cc_start: 0.7260 (mmm) cc_final: 0.6996 (mmm) REVERT: I 104 MET cc_start: 0.8373 (ttt) cc_final: 0.8079 (ttt) REVERT: I 121 LYS cc_start: 0.8269 (mttp) cc_final: 0.7970 (tttm) REVERT: H 56 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7686 (pp20) REVERT: H 100 ASP cc_start: 0.8789 (t0) cc_final: 0.8435 (t0) REVERT: L 87 TYR cc_start: 0.6613 (m-80) cc_final: 0.6382 (m-10) outliers start: 40 outliers final: 28 residues processed: 269 average time/residue: 0.2886 time to fit residues: 116.8785 Evaluate side-chains 237 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 620 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 584 GLU 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 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain G residue 75 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 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 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 51 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 640 GLN B 653 GLN C 85 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** 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 = 0.4096 r_free = 0.4096 target = 0.164302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134760 restraints weight = 25729.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136492 restraints weight = 23231.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138249 restraints weight = 18578.466| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17415 Z= 0.188 Angle : 0.757 22.795 23837 Z= 0.340 Chirality : 0.060 1.808 2941 Planarity : 0.003 0.042 2846 Dihedral : 11.332 105.630 4331 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.83 % Allowed : 12.41 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.19), residues: 1934 helix: 0.66 (0.27), residues: 375 sheet: 0.49 (0.24), residues: 499 loop : -0.29 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 35 HIS 0.005 0.001 HIS G 105 PHE 0.018 0.002 PHE C 382 TYR 0.016 0.002 TYR A 638 ARG 0.013 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00779 ( 63) link_NAG-ASN : angle 3.90454 ( 189) link_ALPHA1-6 : bond 0.00566 ( 6) link_ALPHA1-6 : angle 1.76139 ( 18) link_BETA1-4 : bond 0.00426 ( 29) link_BETA1-4 : angle 1.27367 ( 87) link_ALPHA1-2 : bond 0.00769 ( 3) link_ALPHA1-2 : angle 1.65488 ( 9) link_ALPHA1-3 : bond 0.01286 ( 7) link_ALPHA1-3 : angle 3.25992 ( 21) hydrogen bonds : bond 0.06125 ( 408) hydrogen bonds : angle 5.40592 ( 1149) SS BOND : bond 0.00372 ( 38) SS BOND : angle 1.58401 ( 76) covalent geometry : bond 0.00435 (17269) covalent geometry : angle 0.65843 (23437) *********************** 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 273 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 607 ASN cc_start: 0.7611 (p0) cc_final: 0.7158 (p0) REVERT: B 615 SER cc_start: 0.8764 (t) cc_final: 0.8496 (m) REVERT: C 337 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8432 (m) REVERT: F 590 GLN cc_start: 0.9114 (tp40) cc_final: 0.8826 (tp40) REVERT: F 621 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6265 (tm-30) REVERT: G 97 LYS cc_start: 0.8234 (mttp) cc_final: 0.7808 (mttp) REVERT: I 104 MET cc_start: 0.8385 (ttt) cc_final: 0.8161 (ttt) REVERT: I 121 LYS cc_start: 0.8340 (mttp) cc_final: 0.8021 (tttm) REVERT: I 355 ASN cc_start: 0.7759 (m-40) cc_final: 0.7525 (t0) REVERT: H 32 GLN cc_start: 0.6895 (mt0) cc_final: 0.6637 (mt0) REVERT: H 56 GLU cc_start: 0.8118 (pm20) cc_final: 0.7799 (pp20) REVERT: H 100 ASP cc_start: 0.8666 (t0) cc_final: 0.8454 (t0) outliers start: 49 outliers final: 35 residues processed: 253 average time/residue: 0.2773 time to fit residues: 106.4953 Evaluate side-chains 227 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 1.937 ------------------------------------------------------------------------------- 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 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 641 ILE 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 F residue 537 LEU Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 75 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 434 MET Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 272 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 145 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 126 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 0.0770 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 0.0370 chunk 117 optimal weight: 0.0370 overall best weight: 0.2294 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN ** G 287 GLN ** 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 = 0.4134 r_free = 0.4134 target = 0.167589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.137530 restraints weight = 25378.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.139968 restraints weight = 21195.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141607 restraints weight = 16627.214| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 17415 Z= 0.111 Angle : 0.680 21.301 23837 Z= 0.305 Chirality : 0.050 0.858 2941 Planarity : 0.003 0.058 2846 Dihedral : 10.056 100.294 4331 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.54 % Allowed : 14.25 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1934 helix: 0.86 (0.27), residues: 375 sheet: 0.69 (0.24), residues: 503 loop : -0.28 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP L 35 HIS 0.004 0.001 HIS G 105 PHE 0.020 0.001 PHE C 382 TYR 0.014 0.001 TYR B 638 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 63) link_NAG-ASN : angle 3.47458 ( 189) link_ALPHA1-6 : bond 0.00816 ( 6) link_ALPHA1-6 : angle 1.57750 ( 18) link_BETA1-4 : bond 0.00437 ( 29) link_BETA1-4 : angle 1.18046 ( 87) link_ALPHA1-2 : bond 0.00708 ( 3) link_ALPHA1-2 : angle 1.62195 ( 9) link_ALPHA1-3 : bond 0.01292 ( 7) link_ALPHA1-3 : angle 3.21601 ( 21) hydrogen bonds : bond 0.04785 ( 408) hydrogen bonds : angle 4.93343 ( 1149) SS BOND : bond 0.00467 ( 38) SS BOND : angle 1.70421 ( 76) covalent geometry : bond 0.00233 (17269) covalent geometry : angle 0.58827 (23437) *********************** 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 262 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 ASN cc_start: 0.7968 (p0) cc_final: 0.7708 (p0) REVERT: B 595 ILE cc_start: 0.8678 (pt) cc_final: 0.8407 (mt) REVERT: B 607 ASN cc_start: 0.7591 (p0) cc_final: 0.7192 (p0) REVERT: B 615 SER cc_start: 0.8776 (t) cc_final: 0.8500 (m) REVERT: B 626 MET cc_start: 0.7669 (mtp) cc_final: 0.7337 (mtt) REVERT: B 632 ASP cc_start: 0.8006 (t70) cc_final: 0.7572 (t70) REVERT: C 337 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8244 (m) REVERT: C 434 MET cc_start: 0.7196 (tmm) cc_final: 0.6966 (tmm) REVERT: G 97 LYS cc_start: 0.8184 (mttp) cc_final: 0.7750 (mttp) REVERT: I 121 LYS cc_start: 0.8311 (mttp) cc_final: 0.7970 (tttm) REVERT: H 32 GLN cc_start: 0.6782 (mt0) cc_final: 0.6561 (mt0) REVERT: H 56 GLU cc_start: 0.8111 (pm20) cc_final: 0.7877 (pp20) REVERT: H 100 ASP cc_start: 0.8685 (t0) cc_final: 0.8469 (t0) outliers start: 44 outliers final: 33 residues processed: 248 average time/residue: 0.2732 time to fit residues: 103.1696 Evaluate side-chains 227 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 1.892 ------------------------------------------------------------------------------- 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 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 605 CYS 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 97 LYS 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 F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 501 CYS Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.0470 chunk 64 optimal weight: 7.9990 chunk 56 optimal weight: 0.4980 chunk 158 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 658 GLN ** G 287 GLN ** 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 = 0.4115 r_free = 0.4115 target = 0.165741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136834 restraints weight = 25841.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138632 restraints weight = 24361.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140206 restraints weight = 18267.553| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17415 Z= 0.124 Angle : 0.668 17.993 23837 Z= 0.302 Chirality : 0.049 0.746 2941 Planarity : 0.003 0.041 2846 Dihedral : 9.248 98.132 4331 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.06 % Allowed : 14.31 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 1934 helix: 0.98 (0.28), residues: 376 sheet: 0.63 (0.24), residues: 505 loop : -0.28 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 35 HIS 0.004 0.001 HIS L 39 PHE 0.016 0.001 PHE C 382 TYR 0.025 0.001 TYR A 638 ARG 0.005 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 63) link_NAG-ASN : angle 3.25206 ( 189) link_ALPHA1-6 : bond 0.00814 ( 6) link_ALPHA1-6 : angle 1.39777 ( 18) link_BETA1-4 : bond 0.00445 ( 29) link_BETA1-4 : angle 1.21442 ( 87) link_ALPHA1-2 : bond 0.00657 ( 3) link_ALPHA1-2 : angle 1.65712 ( 9) link_ALPHA1-3 : bond 0.01202 ( 7) link_ALPHA1-3 : angle 3.12630 ( 21) hydrogen bonds : bond 0.04471 ( 408) hydrogen bonds : angle 4.82395 ( 1149) SS BOND : bond 0.00340 ( 38) SS BOND : angle 1.59575 ( 76) covalent geometry : bond 0.00280 (17269) covalent geometry : angle 0.58614 (23437) *********************** 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 258 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6825 (p0) REVERT: B 607 ASN cc_start: 0.7463 (p0) cc_final: 0.7157 (p0) REVERT: B 615 SER cc_start: 0.8765 (t) cc_final: 0.8506 (m) REVERT: B 632 ASP cc_start: 0.7999 (t70) cc_final: 0.7589 (t70) REVERT: C 337 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8241 (m) REVERT: C 434 MET cc_start: 0.7236 (tmm) cc_final: 0.7002 (tmm) REVERT: G 97 LYS cc_start: 0.8220 (mttp) cc_final: 0.7806 (mttp) REVERT: I 121 LYS cc_start: 0.8282 (mttp) cc_final: 0.7968 (tttm) REVERT: H 32 GLN cc_start: 0.6800 (mt0) cc_final: 0.6577 (mt0) REVERT: H 95 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: H 100 ASP cc_start: 0.8675 (t0) cc_final: 0.8458 (t0) outliers start: 53 outliers final: 36 residues processed: 243 average time/residue: 0.2713 time to fit residues: 102.0492 Evaluate side-chains 232 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 635 ILE 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 97 LYS Chi-restraints excluded: chain C residue 132 THR 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 F residue 575 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 75 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 434 MET Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 190 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 155 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN G 67 ASN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 302 ASN ** 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 = 0.4029 r_free = 0.4029 target = 0.155682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123127 restraints weight = 25415.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125957 restraints weight = 20539.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127246 restraints weight = 16726.326| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 17415 Z= 0.279 Angle : 0.843 16.864 23837 Z= 0.391 Chirality : 0.053 0.629 2941 Planarity : 0.004 0.040 2846 Dihedral : 9.490 107.318 4331 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.04 % Allowed : 15.18 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 1934 helix: 0.59 (0.28), residues: 379 sheet: 0.07 (0.23), residues: 493 loop : -0.50 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 35 HIS 0.008 0.002 HIS L 39 PHE 0.025 0.002 PHE C 382 TYR 0.027 0.002 TYR C 191 ARG 0.006 0.001 ARG I 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00871 ( 63) link_NAG-ASN : angle 3.43612 ( 189) link_ALPHA1-6 : bond 0.00667 ( 6) link_ALPHA1-6 : angle 1.64240 ( 18) link_BETA1-4 : bond 0.00510 ( 29) link_BETA1-4 : angle 1.44020 ( 87) link_ALPHA1-2 : bond 0.00475 ( 3) link_ALPHA1-2 : angle 2.02096 ( 9) link_ALPHA1-3 : bond 0.01098 ( 7) link_ALPHA1-3 : angle 3.34538 ( 21) hydrogen bonds : bond 0.05611 ( 408) hydrogen bonds : angle 5.20784 ( 1149) SS BOND : bond 0.00451 ( 38) SS BOND : angle 2.03281 ( 76) covalent geometry : bond 0.00658 (17269) covalent geometry : angle 0.76942 (23437) *********************** 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 272 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 202 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 612 SER cc_start: 0.8668 (m) cc_final: 0.8309 (p) REVERT: B 615 SER cc_start: 0.8963 (t) cc_final: 0.8725 (m) REVERT: B 658 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7328 (tp40) REVERT: C 104 MET cc_start: 0.8603 (ttm) cc_final: 0.8369 (ttt) REVERT: C 426 MET cc_start: 0.8405 (tpt) cc_final: 0.7959 (tpt) REVERT: F 530 MET cc_start: 0.8162 (tpp) cc_final: 0.7783 (mtp) REVERT: F 657 GLU cc_start: 0.8073 (tp30) cc_final: 0.7864 (tm-30) REVERT: G 97 LYS cc_start: 0.8350 (mttp) cc_final: 0.7876 (mttp) REVERT: G 102 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: I 340 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7462 (tm-30) outliers start: 70 outliers final: 56 residues processed: 255 average time/residue: 0.2696 time to fit residues: 105.6327 Evaluate side-chains 236 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 624 ASP Chi-restraints excluded: chain A residue 635 ILE 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 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 THR 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 357 THR 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 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 67 ASN 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 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 75 VAL 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 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 334 SER Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 426 MET 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 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 68 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.158389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.126001 restraints weight = 25037.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128300 restraints weight = 19956.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.129171 restraints weight = 15765.977| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3845 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= 0.152 Angle : 0.725 17.289 23837 Z= 0.331 Chirality : 0.048 0.488 2941 Planarity : 0.003 0.034 2846 Dihedral : 8.945 109.389 4331 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.83 % Allowed : 16.79 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1934 helix: 0.83 (0.28), residues: 381 sheet: 0.24 (0.23), residues: 478 loop : -0.48 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 35 HIS 0.004 0.001 HIS G 66 PHE 0.021 0.001 PHE C 382 TYR 0.020 0.001 TYR H 58 ARG 0.007 0.000 ARG G 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 63) link_NAG-ASN : angle 3.41358 ( 189) link_ALPHA1-6 : bond 0.00721 ( 6) link_ALPHA1-6 : angle 1.46896 ( 18) link_BETA1-4 : bond 0.00416 ( 29) link_BETA1-4 : angle 1.25065 ( 87) link_ALPHA1-2 : bond 0.00450 ( 3) link_ALPHA1-2 : angle 1.88996 ( 9) link_ALPHA1-3 : bond 0.01154 ( 7) link_ALPHA1-3 : angle 3.16162 ( 21) hydrogen bonds : bond 0.04673 ( 408) hydrogen bonds : angle 4.85816 ( 1149) SS BOND : bond 0.00418 ( 38) SS BOND : angle 1.74666 ( 76) covalent geometry : bond 0.00355 (17269) covalent geometry : angle 0.64234 (23437) *********************** 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 242 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 612 SER cc_start: 0.8711 (m) cc_final: 0.8332 (p) REVERT: B 615 SER cc_start: 0.8972 (t) cc_final: 0.8747 (m) REVERT: C 95 MET cc_start: 0.8089 (ptt) cc_final: 0.7834 (ptt) REVERT: C 104 MET cc_start: 0.8539 (ttm) cc_final: 0.8178 (ttt) REVERT: F 530 MET cc_start: 0.8300 (tpp) cc_final: 0.7725 (mtp) REVERT: G 97 LYS cc_start: 0.8330 (mttp) cc_final: 0.7876 (mttp) REVERT: G 102 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: G 161 MET cc_start: 0.8282 (tpt) cc_final: 0.7844 (tpt) REVERT: G 277 ILE cc_start: 0.8643 (mm) cc_final: 0.8441 (mt) outliers start: 49 outliers final: 38 residues processed: 228 average time/residue: 0.2709 time to fit residues: 95.8159 Evaluate side-chains 218 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 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 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 205 CYS 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 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU 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 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 123 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 L residue 85 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 0.2980 chunk 129 optimal weight: 0.8980 chunk 167 optimal weight: 0.4980 chunk 28 optimal weight: 0.2980 chunk 146 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.160557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127915 restraints weight = 25021.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132525 restraints weight = 19488.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134043 restraints weight = 14629.878| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17415 Z= 0.119 Angle : 0.675 13.990 23837 Z= 0.309 Chirality : 0.048 0.481 2941 Planarity : 0.003 0.037 2846 Dihedral : 8.316 111.111 4331 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.00 % Allowed : 17.31 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 1934 helix: 0.99 (0.28), residues: 382 sheet: 0.26 (0.23), residues: 484 loop : -0.38 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP G 69 HIS 0.004 0.001 HIS I 66 PHE 0.017 0.001 PHE C 382 TYR 0.034 0.001 TYR A 638 ARG 0.008 0.000 ARG A 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 63) link_NAG-ASN : angle 2.92790 ( 189) link_ALPHA1-6 : bond 0.00723 ( 6) link_ALPHA1-6 : angle 1.49550 ( 18) link_BETA1-4 : bond 0.00448 ( 29) link_BETA1-4 : angle 1.19141 ( 87) link_ALPHA1-2 : bond 0.00484 ( 3) link_ALPHA1-2 : angle 1.80589 ( 9) link_ALPHA1-3 : bond 0.01143 ( 7) link_ALPHA1-3 : angle 3.00071 ( 21) hydrogen bonds : bond 0.03989 ( 408) hydrogen bonds : angle 4.66918 ( 1149) SS BOND : bond 0.00411 ( 38) SS BOND : angle 1.62039 ( 76) covalent geometry : bond 0.00272 (17269) covalent geometry : angle 0.60759 (23437) *********************** 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 244 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 612 SER cc_start: 0.8732 (m) cc_final: 0.8383 (p) REVERT: B 615 SER cc_start: 0.8987 (t) cc_final: 0.8718 (m) REVERT: C 104 MET cc_start: 0.8510 (ttm) cc_final: 0.8221 (ttt) REVERT: F 530 MET cc_start: 0.8258 (tpp) cc_final: 0.7666 (mtp) REVERT: G 97 LYS cc_start: 0.8317 (mttp) cc_final: 0.7871 (mttp) REVERT: G 102 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6079 (mp0) REVERT: G 161 MET cc_start: 0.8440 (tpt) cc_final: 0.7993 (tpt) REVERT: G 215 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8126 (tp) REVERT: H 79 TYR cc_start: 0.7984 (m-10) cc_final: 0.7699 (m-10) outliers start: 52 outliers final: 41 residues processed: 226 average time/residue: 0.2515 time to fit residues: 88.8764 Evaluate side-chains 220 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 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 605 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 CYS 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 433 CYS Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 646 LEU 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 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 I residue 75 VAL Chi-restraints excluded: chain I residue 123 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 356 ASN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 75 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 95 optimal weight: 0.0870 chunk 186 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 ** 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 = 0.4086 r_free = 0.4086 target = 0.160617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128563 restraints weight = 25244.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131467 restraints weight = 19273.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133599 restraints weight = 15772.653| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17415 Z= 0.118 Angle : 0.667 14.131 23837 Z= 0.307 Chirality : 0.047 0.475 2941 Planarity : 0.003 0.037 2846 Dihedral : 8.027 111.220 4331 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.89 % Allowed : 18.00 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 1934 helix: 1.05 (0.28), residues: 382 sheet: 0.36 (0.24), residues: 474 loop : -0.39 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 35 HIS 0.003 0.001 HIS G 105 PHE 0.017 0.001 PHE C 382 TYR 0.027 0.001 TYR A 638 ARG 0.006 0.000 ARG G 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 63) link_NAG-ASN : angle 2.80252 ( 189) link_ALPHA1-6 : bond 0.00700 ( 6) link_ALPHA1-6 : angle 1.49012 ( 18) link_BETA1-4 : bond 0.00452 ( 29) link_BETA1-4 : angle 1.20036 ( 87) link_ALPHA1-2 : bond 0.00530 ( 3) link_ALPHA1-2 : angle 1.79599 ( 9) link_ALPHA1-3 : bond 0.01132 ( 7) link_ALPHA1-3 : angle 2.96557 ( 21) hydrogen bonds : bond 0.03840 ( 408) hydrogen bonds : angle 4.65183 ( 1149) SS BOND : bond 0.00366 ( 38) SS BOND : angle 1.59608 ( 76) covalent geometry : bond 0.00270 (17269) covalent geometry : angle 0.60397 (23437) *********************** 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 229 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 1.694 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: 0.7453 (OUTLIER) cc_final: 0.6777 (p0) REVERT: B 530 MET cc_start: 0.8174 (mtp) cc_final: 0.7737 (mtp) REVERT: B 612 SER cc_start: 0.8790 (m) cc_final: 0.8399 (p) REVERT: B 615 SER cc_start: 0.8915 (t) cc_final: 0.8615 (m) REVERT: C 104 MET cc_start: 0.8556 (ttm) cc_final: 0.8195 (ttt) REVERT: G 97 LYS cc_start: 0.8323 (mttp) cc_final: 0.7874 (mttp) REVERT: G 102 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6075 (mp0) REVERT: G 161 MET cc_start: 0.8452 (tpt) cc_final: 0.8034 (tpt) REVERT: G 215 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8000 (tp) REVERT: H 79 TYR cc_start: 0.7973 (m-10) cc_final: 0.7705 (m-10) outliers start: 50 outliers final: 39 residues processed: 214 average time/residue: 0.2583 time to fit residues: 86.5326 Evaluate side-chains 214 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 653 GLN 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 97 LYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 205 CYS 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 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU 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 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 75 VAL Chi-restraints excluded: chain I residue 123 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 481 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 71 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.159626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.127853 restraints weight = 25124.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129574 restraints weight = 19259.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131774 restraints weight = 16517.399| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17415 Z= 0.137 Angle : 0.681 13.567 23837 Z= 0.314 Chirality : 0.047 0.468 2941 Planarity : 0.003 0.039 2846 Dihedral : 7.871 112.084 4331 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.94 % Allowed : 18.18 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 1934 helix: 1.16 (0.28), residues: 375 sheet: 0.37 (0.24), residues: 466 loop : -0.43 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 35 HIS 0.003 0.001 HIS G 105 PHE 0.018 0.001 PHE C 382 TYR 0.026 0.001 TYR A 638 ARG 0.009 0.000 ARG H 100B Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 63) link_NAG-ASN : angle 2.74750 ( 189) link_ALPHA1-6 : bond 0.00663 ( 6) link_ALPHA1-6 : angle 1.53190 ( 18) link_BETA1-4 : bond 0.00442 ( 29) link_BETA1-4 : angle 1.21060 ( 87) link_ALPHA1-2 : bond 0.00504 ( 3) link_ALPHA1-2 : angle 1.80737 ( 9) link_ALPHA1-3 : bond 0.01071 ( 7) link_ALPHA1-3 : angle 2.91684 ( 21) hydrogen bonds : bond 0.03947 ( 408) hydrogen bonds : angle 4.65001 ( 1149) SS BOND : bond 0.00385 ( 38) SS BOND : angle 1.62225 ( 76) covalent geometry : bond 0.00320 (17269) covalent geometry : angle 0.62178 (23437) ********************** 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 226 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.6799 (p0) REVERT: B 612 SER cc_start: 0.8729 (m) cc_final: 0.8332 (p) REVERT: B 615 SER cc_start: 0.8931 (t) cc_final: 0.8616 (m) REVERT: C 104 MET cc_start: 0.8495 (ttm) cc_final: 0.8197 (ttt) REVERT: C 434 MET cc_start: 0.7306 (tmm) cc_final: 0.7072 (tmm) REVERT: G 97 LYS cc_start: 0.8309 (mttp) cc_final: 0.7846 (mttp) REVERT: G 102 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6011 (mp0) REVERT: G 161 MET cc_start: 0.8424 (tpt) cc_final: 0.8015 (tpt) REVERT: G 215 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8019 (tp) REVERT: H 79 TYR cc_start: 0.7973 (m-10) cc_final: 0.7705 (m-10) outliers start: 51 outliers final: 43 residues processed: 211 average time/residue: 0.2554 time to fit residues: 85.1050 Evaluate side-chains 220 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 1.761 ------------------------------------------------------------------------------- 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 622 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 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 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 97 LYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 205 CYS 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 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU 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 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 75 VAL Chi-restraints excluded: chain I residue 123 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 481 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 181 optimal weight: 0.0050 chunk 114 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 47 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 ** 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 = 0.4114 r_free = 0.4114 target = 0.165112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.131179 restraints weight = 25450.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135061 restraints weight = 19428.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.136617 restraints weight = 14900.466| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17415 Z= 0.114 Angle : 0.651 13.519 23837 Z= 0.303 Chirality : 0.046 0.464 2941 Planarity : 0.003 0.040 2846 Dihedral : 7.481 112.171 4331 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.65 % Allowed : 18.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1934 helix: 1.24 (0.28), residues: 375 sheet: 0.37 (0.24), residues: 497 loop : -0.35 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 35 HIS 0.003 0.001 HIS G 105 PHE 0.016 0.001 PHE C 382 TYR 0.022 0.001 TYR A 638 ARG 0.009 0.000 ARG H 100B Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 63) link_NAG-ASN : angle 2.65880 ( 189) link_ALPHA1-6 : bond 0.00746 ( 6) link_ALPHA1-6 : angle 1.55432 ( 18) link_BETA1-4 : bond 0.00441 ( 29) link_BETA1-4 : angle 1.18970 ( 87) link_ALPHA1-2 : bond 0.00535 ( 3) link_ALPHA1-2 : angle 1.78140 ( 9) link_ALPHA1-3 : bond 0.01166 ( 7) link_ALPHA1-3 : angle 2.13755 ( 21) hydrogen bonds : bond 0.03694 ( 408) hydrogen bonds : angle 4.56167 ( 1149) SS BOND : bond 0.00379 ( 38) SS BOND : angle 1.51913 ( 76) covalent geometry : bond 0.00260 (17269) covalent geometry : angle 0.59500 (23437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4842.16 seconds wall clock time: 86 minutes 32.13 seconds (5192.13 seconds total)