Starting phenix.real_space_refine on Wed Mar 4 20:42:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8x_23239/03_2026/7l8x_23239.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8x_23239/03_2026/7l8x_23239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l8x_23239/03_2026/7l8x_23239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8x_23239/03_2026/7l8x_23239.map" model { file = "/net/cci-nas-00/data/ceres_data/7l8x_23239/03_2026/7l8x_23239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8x_23239/03_2026/7l8x_23239.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 104 5.16 5 C 10010 2.51 5 N 2703 2.21 5 O 3273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16090 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 3507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3507 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 20, 'TRANS': 423} Chain breaks: 2 Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1155 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "C" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3461 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "E" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3371 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 5 Chain: "F" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1101 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain: "G" 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: "I" 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: 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: "K" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 2, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: 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: "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: 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: "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: 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: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" 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: 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 Time building chain proxies: 3.81, per 1000 atoms: 0.24 Number of scatterers: 16090 At special positions: 0 Unit cell: (129.78, 128.75, 122.57, 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 104 16.00 O 3273 8.00 N 2703 7.00 C 10010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 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 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN T 4 " - " MAN T 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 9 " " BMA T 3 " - " MAN T 6 " " BMA b 3 " - " MAN b 6 " BETA1-3 " MAN K 7 " - " BMA K 8 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 295 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 160 " " NAG A 610 " - " ASN A 197 " " NAG A 611 " - " ASN A 133 " " NAG A 612 " - " ASN A 355 " " NAG A 613 " - " ASN A 289 " " NAG A 614 " - " ASN A 363 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 448 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 160 " " NAG C 608 " - " ASN C 197 " " NAG C 609 " - " ASN C 133 " " NAG C 610 " - " ASN C 355 " " NAG C 611 " - " ASN C 289 " " NAG C 612 " - " ASN C 363 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 241 " " NAG E 603 " - " ASN E 276 " " NAG E 604 " - " ASN E 339 " " NAG E 605 " - " ASN E 448 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 156 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 133 " " NAG E 610 " - " ASN E 355 " " NAG E 611 " - " ASN E 289 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 392 " " NAG I 1 " - " ASN A 386 " " NAG J 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN B 611 " " NAG O 1 " - " ASN C 88 " " NAG P 1 " - " ASN C 392 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN C 332 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN D 611 " " NAG W 1 " - " ASN E 88 " " NAG X 1 " - " ASN E 392 " " NAG Y 1 " - " ASN E 386 " " NAG Z 1 " - " ASN E 332 " " NAG a 1 " - " ASN E 295 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 197 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN F 611 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 646.3 milliseconds 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 33 sheets defined 31.2% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.550A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.995A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.336A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 545 removed outlier: 3.642A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 558 removed outlier: 3.592A pdb=" N LEU B 556 " --> pdb=" O GLN B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 566 removed outlier: 3.636A pdb=" N LEU B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.634A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.023A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.413A 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 476 through 484 removed outlier: 4.739A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.197A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 569 through 597 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'H' and resid 99 through 103 Processing helix chain 'E' and resid 100 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 334 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.980A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.564A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.405A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 557 removed outlier: 4.017A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 568 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 657 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.315A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.467A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.646A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 257 removed outlier: 4.344A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.421A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AB1, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.172A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.420A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.230A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.114A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.326A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.104A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 304 through 309 Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.905A pdb=" N UNK H 46 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N UNK H 37 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N UNK H 50 " --> pdb=" O UNK H 33 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N UNK H 33 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.905A pdb=" N UNK H 46 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N UNK H 37 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N UNK H 50 " --> pdb=" O UNK H 33 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N UNK H 33 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'L' and resid 43 through 45 Processing sheet with id=AC7, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.479A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.532A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.114A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD2, first strand: chain 'E' and resid 171 through 177 Processing sheet with id=AD3, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.069A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.673A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.062A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.481A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.057A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.817A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.057A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.786A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.481A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.062A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.754A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3151 1.32 - 1.45: 5158 1.45 - 1.59: 7855 1.59 - 1.73: 62 1.73 - 1.87: 133 Bond restraints: 16359 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.45e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.35e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.30e+01 bond pdb=" CB HIS E 105 " pdb=" CG HIS E 105 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.09e+01 bond pdb=" CB ILE A 396 " pdb=" CG1 ILE A 396 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.05e+01 ... (remaining 16354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 20248 2.86 - 5.72: 1848 5.72 - 8.57: 143 8.57 - 11.43: 8 11.43 - 14.29: 2 Bond angle restraints: 22249 Sorted by residual: angle pdb=" N MET E 100 " pdb=" CA MET E 100 " pdb=" C MET E 100 " ideal model delta sigma weight residual 114.62 100.33 14.29 1.14e+00 7.69e-01 1.57e+02 angle pdb=" N THR C 464 " pdb=" CA THR C 464 " pdb=" C THR C 464 " ideal model delta sigma weight residual 114.56 102.88 11.68 1.27e+00 6.20e-01 8.46e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 127.87 -8.31 1.02e+00 9.61e-01 6.64e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.51 -7.95 1.01e+00 9.80e-01 6.20e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.44 -7.88 1.01e+00 9.80e-01 6.09e+01 ... (remaining 22244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 10814 21.15 - 42.30: 236 42.30 - 63.45: 78 63.45 - 84.60: 39 84.60 - 105.75: 22 Dihedral angle restraints: 11189 sinusoidal: 5573 harmonic: 5616 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 160.43 -67.43 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.41 -60.41 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS E 74 " pdb=" SG CYS E 74 " pdb=" SG CYS F 561 " pdb=" CB CYS F 561 " ideal model delta sinusoidal sigma weight residual 93.00 46.11 46.89 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 11186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 2748 0.329 - 0.657: 122 0.657 - 0.986: 0 0.986 - 1.314: 0 1.314 - 1.643: 1 Chirality restraints: 2871 Sorted by residual: chirality pdb=" C1 MAN K 7 " pdb=" O6 BMA K 3 " pdb=" C2 MAN K 7 " pdb=" O5 MAN K 7 " both_signs ideal model delta sigma weight residual False 2.40 0.76 1.64 2.00e-02 2.50e+03 6.75e+03 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.95e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.74e+02 ... (remaining 2868 not shown) Planarity restraints: 2773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG Z 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " 0.113 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " -0.348 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG C 604 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.335 2.00e-02 2.50e+03 2.88e-01 1.03e+03 pdb=" C7 NAG K 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.103 2.00e-02 2.50e+03 ... (remaining 2770 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3721 2.80 - 3.33: 14980 3.33 - 3.85: 25601 3.85 - 4.38: 30373 4.38 - 4.90: 48358 Nonbonded interactions: 123033 Sorted by model distance: nonbonded pdb=" O3 NAG A 605 " pdb=" O7 NAG A 605 " model vdw 2.275 3.040 nonbonded pdb=" O3 NAG C 602 " pdb=" O7 NAG C 602 " model vdw 2.324 3.040 nonbonded pdb=" N HIS A 72 " pdb=" O HIS A 72 " model vdw 2.345 2.496 nonbonded pdb=" N GLY D 597 " pdb=" O GLY D 597 " model vdw 2.393 2.496 nonbonded pdb=" N MET E 100 " pdb=" N VAL E 101 " model vdw 2.406 2.560 ... (remaining 123028 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 33 through 60 or resid 66 through 162 or resid 170 through \ 185 or resid 189 through 457 or resid 462 through 611)) selection = (chain 'C' and (resid 33 through 162 or resid 170 through 185 or resid 189 throu \ gh 457 or resid 462 through 611)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 520 through 546 or resid 564 through 657 or resid 701)) selection = (chain 'D' and (resid 520 through 657 or resid 701)) selection = (chain 'F' and (resid 520 through 546 or resid 564 through 701)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = (chain 'H' and resid 19 through 117) selection = chain 'L' } ncs_group { reference = chain 'T' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.480 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.022 0.144 16496 Z= 1.179 Angle : 1.737 14.290 22626 Z= 1.093 Chirality : 0.141 1.643 2871 Planarity : 0.018 0.300 2708 Dihedral : 11.797 105.749 7431 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1687 helix: 0.58 (0.23), residues: 436 sheet: 0.78 (0.25), residues: 393 loop : 0.78 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 557 TYR 0.060 0.008 TYR C 40 PHE 0.031 0.006 PHE E 353 TRP 0.052 0.010 TRP B 571 HIS 0.008 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.02151 (16359) covalent geometry : angle 1.69745 (22249) SS BOND : bond 0.00794 ( 34) SS BOND : angle 3.01231 ( 68) hydrogen bonds : bond 0.17655 ( 645) hydrogen bonds : angle 7.55792 ( 1740) link_ALPHA1-2 : bond 0.05505 ( 4) link_ALPHA1-2 : angle 3.57863 ( 12) link_ALPHA1-3 : bond 0.06477 ( 3) link_ALPHA1-3 : angle 3.68742 ( 9) link_ALPHA1-6 : bond 0.04477 ( 4) link_ALPHA1-6 : angle 5.76101 ( 12) link_BETA1-3 : bond 0.00465 ( 1) link_BETA1-3 : angle 1.80649 ( 3) link_BETA1-4 : bond 0.06199 ( 26) link_BETA1-4 : angle 4.31725 ( 78) link_NAG-ASN : bond 0.07023 ( 65) link_NAG-ASN : angle 2.68259 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 568 LEU cc_start: 0.7830 (tp) cc_final: 0.7623 (tt) outliers start: 0 outliers final: 2 residues processed: 492 average time/residue: 0.6086 time to fit residues: 330.9203 Evaluate side-chains 205 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain D residue 573 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 72 HIS B 575 GLN B 577 GLN B 658 GLN C 33 ASN C 105 HIS C 114 GLN C 377 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 577 GLN D 651 ASN E 80 ASN E 99 ASN E 130 GLN E 195 ASN F 591 GLN F 625 ASN F 630 GLN F 640 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.113105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.093106 restraints weight = 33064.743| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 4.42 r_work: 0.3212 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16496 Z= 0.178 Angle : 0.860 14.986 22626 Z= 0.406 Chirality : 0.050 0.602 2871 Planarity : 0.004 0.041 2708 Dihedral : 9.126 86.441 4173 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 5.29 % Allowed : 14.11 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1687 helix: 1.91 (0.25), residues: 427 sheet: 0.64 (0.22), residues: 464 loop : 0.25 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 617 TYR 0.027 0.002 TYR D 643 PHE 0.026 0.002 PHE E 383 TRP 0.025 0.002 TRP B 610 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00385 (16359) covalent geometry : angle 0.79675 (22249) SS BOND : bond 0.00344 ( 34) SS BOND : angle 1.31452 ( 68) hydrogen bonds : bond 0.05973 ( 645) hydrogen bonds : angle 5.58723 ( 1740) link_ALPHA1-2 : bond 0.00972 ( 4) link_ALPHA1-2 : angle 2.36024 ( 12) link_ALPHA1-3 : bond 0.01046 ( 3) link_ALPHA1-3 : angle 2.44469 ( 9) link_ALPHA1-6 : bond 0.01480 ( 4) link_ALPHA1-6 : angle 2.14456 ( 12) link_BETA1-3 : bond 0.01087 ( 1) link_BETA1-3 : angle 2.67252 ( 3) link_BETA1-4 : bond 0.00560 ( 26) link_BETA1-4 : angle 2.49305 ( 78) link_NAG-ASN : bond 0.00527 ( 65) link_NAG-ASN : angle 3.04603 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 277 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7864 (t0) cc_final: 0.7263 (t0) REVERT: A 195 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.8050 (p0) REVERT: A 475 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6742 (mmt) REVERT: B 568 LEU cc_start: 0.8172 (tp) cc_final: 0.7884 (tt) REVERT: B 610 TRP cc_start: 0.7364 (t-100) cc_final: 0.7011 (t60) REVERT: B 623 TRP cc_start: 0.5383 (OUTLIER) cc_final: 0.4855 (m100) REVERT: B 638 TYR cc_start: 0.8048 (m-80) cc_final: 0.7618 (m-10) REVERT: B 647 GLU cc_start: 0.8777 (tt0) cc_final: 0.8575 (tm-30) REVERT: B 649 SER cc_start: 0.8728 (t) cc_final: 0.8497 (p) REVERT: C 150 MET cc_start: 0.8330 (mmm) cc_final: 0.8115 (mmm) REVERT: C 230 ASP cc_start: 0.8640 (t0) cc_final: 0.8201 (t0) REVERT: C 272 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8717 (mp) REVERT: C 280 ASN cc_start: 0.7548 (m-40) cc_final: 0.7315 (m-40) REVERT: C 430 ILE cc_start: 0.8589 (mm) cc_final: 0.8265 (pp) REVERT: D 543 ASN cc_start: 0.9166 (m110) cc_final: 0.8839 (m-40) REVERT: D 590 GLN cc_start: 0.7989 (tp40) cc_final: 0.7704 (tt0) REVERT: D 630 GLN cc_start: 0.8904 (mt0) cc_final: 0.8573 (mp10) REVERT: D 648 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8740 (pt0) REVERT: E 123 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8070 (t) REVERT: E 150 MET cc_start: 0.7465 (mpp) cc_final: 0.6870 (mpp) REVERT: E 201 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8442 (pp) REVERT: E 320 THR cc_start: 0.8085 (p) cc_final: 0.7863 (t) REVERT: E 342 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8361 (mt) REVERT: E 395 TRP cc_start: 0.7375 (m100) cc_final: 0.6994 (m-90) REVERT: E 492 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8286 (mt-10) REVERT: F 577 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8245 (tm-30) REVERT: F 626 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7909 (ttp) outliers start: 81 outliers final: 24 residues processed: 326 average time/residue: 0.5204 time to fit residues: 190.5752 Evaluate side-chains 217 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 626 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 0.0020 chunk 160 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 overall best weight: 1.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN B 625 ASN C 98 ASN D 653 GLN E 80 ASN E 99 ASN E 425 ASN F 554 ASN F 651 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087416 restraints weight = 35401.427| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 4.32 r_work: 0.3172 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16496 Z= 0.197 Angle : 0.772 13.422 22626 Z= 0.369 Chirality : 0.047 0.280 2871 Planarity : 0.004 0.044 2708 Dihedral : 7.859 80.394 4171 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.62 % Allowed : 16.92 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1687 helix: 1.94 (0.26), residues: 425 sheet: 0.60 (0.22), residues: 468 loop : -0.12 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 500 TYR 0.024 0.002 TYR F 643 PHE 0.019 0.002 PHE E 376 TRP 0.035 0.002 TRP A 35 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00449 (16359) covalent geometry : angle 0.71877 (22249) SS BOND : bond 0.00610 ( 34) SS BOND : angle 1.64968 ( 68) hydrogen bonds : bond 0.05250 ( 645) hydrogen bonds : angle 5.13851 ( 1740) link_ALPHA1-2 : bond 0.00735 ( 4) link_ALPHA1-2 : angle 2.50308 ( 12) link_ALPHA1-3 : bond 0.00945 ( 3) link_ALPHA1-3 : angle 1.32951 ( 9) link_ALPHA1-6 : bond 0.00799 ( 4) link_ALPHA1-6 : angle 2.13557 ( 12) link_BETA1-3 : bond 0.00587 ( 1) link_BETA1-3 : angle 2.74834 ( 3) link_BETA1-4 : bond 0.00501 ( 26) link_BETA1-4 : angle 2.04340 ( 78) link_NAG-ASN : bond 0.00539 ( 65) link_NAG-ASN : angle 2.59332 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 234 time to evaluate : 0.566 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 67 ASN cc_start: 0.7864 (t0) cc_final: 0.7350 (t0) REVERT: A 161 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7459 (ttp) REVERT: A 195 ASN cc_start: 0.8396 (m110) cc_final: 0.8184 (p0) REVERT: A 475 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6865 (mmt) REVERT: B 568 LEU cc_start: 0.8495 (tp) cc_final: 0.8282 (tt) REVERT: B 610 TRP cc_start: 0.7736 (t-100) cc_final: 0.7027 (t60) REVERT: B 622 ILE cc_start: 0.8407 (mm) cc_final: 0.8182 (tt) REVERT: B 623 TRP cc_start: 0.5612 (OUTLIER) cc_final: 0.5125 (m100) REVERT: B 633 LYS cc_start: 0.9450 (tttm) cc_final: 0.9175 (pttm) REVERT: B 649 SER cc_start: 0.8774 (t) cc_final: 0.8553 (p) REVERT: C 151 ARG cc_start: 0.8002 (tpt170) cc_final: 0.7741 (tpt170) REVERT: C 161 MET cc_start: 0.7761 (tpp) cc_final: 0.7316 (tpt) REVERT: C 189 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.6149 (ttpp) REVERT: C 193 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6792 (mm) REVERT: C 230 ASP cc_start: 0.8952 (t0) cc_final: 0.8540 (t70) REVERT: C 280 ASN cc_start: 0.7818 (m-40) cc_final: 0.7454 (m-40) REVERT: C 284 ILE cc_start: 0.8136 (mt) cc_final: 0.7833 (tt) REVERT: C 430 ILE cc_start: 0.8673 (mm) cc_final: 0.8387 (pp) REVERT: C 456 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8437 (tmm-80) REVERT: D 543 ASN cc_start: 0.9307 (m110) cc_final: 0.8944 (m-40) REVERT: D 634 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8399 (mt-10) REVERT: E 49 GLU cc_start: 0.8607 (pm20) cc_final: 0.8335 (mp0) REVERT: E 92 GLU cc_start: 0.8569 (tt0) cc_final: 0.8125 (tm-30) REVERT: E 123 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8265 (t) REVERT: E 125 LEU cc_start: 0.8582 (tp) cc_final: 0.8368 (tt) REVERT: E 150 MET cc_start: 0.7577 (mpp) cc_final: 0.7086 (mpp) REVERT: E 227 LYS cc_start: 0.6218 (OUTLIER) cc_final: 0.5891 (ttmm) REVERT: E 320 THR cc_start: 0.8161 (p) cc_final: 0.7931 (t) REVERT: F 577 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8380 (tm-30) REVERT: F 621 GLU cc_start: 0.8759 (tt0) cc_final: 0.8118 (pt0) outliers start: 86 outliers final: 33 residues processed: 292 average time/residue: 0.5817 time to fit residues: 188.8255 Evaluate side-chains 228 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 456 ARG Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 10 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN C 183 GLN D 577 GLN D 653 GLN E 99 ASN E 425 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.085448 restraints weight = 35436.780| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.28 r_work: 0.3136 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16496 Z= 0.217 Angle : 0.765 13.514 22626 Z= 0.368 Chirality : 0.047 0.291 2871 Planarity : 0.004 0.039 2708 Dihedral : 7.334 75.574 4169 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 4.77 % Allowed : 18.62 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1687 helix: 1.85 (0.26), residues: 424 sheet: 0.51 (0.23), residues: 450 loop : -0.37 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 617 TYR 0.022 0.002 TYR E 173 PHE 0.019 0.002 PHE E 383 TRP 0.021 0.002 TRP D 631 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00500 (16359) covalent geometry : angle 0.71614 (22249) SS BOND : bond 0.00592 ( 34) SS BOND : angle 1.57411 ( 68) hydrogen bonds : bond 0.05000 ( 645) hydrogen bonds : angle 5.05737 ( 1740) link_ALPHA1-2 : bond 0.00666 ( 4) link_ALPHA1-2 : angle 2.46096 ( 12) link_ALPHA1-3 : bond 0.00871 ( 3) link_ALPHA1-3 : angle 1.75356 ( 9) link_ALPHA1-6 : bond 0.00889 ( 4) link_ALPHA1-6 : angle 1.99778 ( 12) link_BETA1-3 : bond 0.00631 ( 1) link_BETA1-3 : angle 2.67902 ( 3) link_BETA1-4 : bond 0.00401 ( 26) link_BETA1-4 : angle 1.88880 ( 78) link_NAG-ASN : bond 0.00424 ( 65) link_NAG-ASN : angle 2.49737 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 215 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7932 (t0) cc_final: 0.7658 (t0) REVERT: A 161 MET cc_start: 0.7920 (tpp) cc_final: 0.7582 (ttp) REVERT: A 475 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.6837 (mmt) REVERT: B 568 LEU cc_start: 0.8509 (tp) cc_final: 0.8298 (tt) REVERT: B 610 TRP cc_start: 0.7922 (t-100) cc_final: 0.7380 (t60) REVERT: B 623 TRP cc_start: 0.5739 (OUTLIER) cc_final: 0.5349 (m100) REVERT: B 633 LYS cc_start: 0.9458 (tttm) cc_final: 0.9208 (pttm) REVERT: B 654 GLU cc_start: 0.8380 (tp30) cc_final: 0.8160 (tp30) REVERT: C 161 MET cc_start: 0.7971 (tpp) cc_final: 0.7363 (tpt) REVERT: C 230 ASP cc_start: 0.9101 (t0) cc_final: 0.8677 (t70) REVERT: C 308 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.6578 (ttp80) REVERT: C 316 TRP cc_start: 0.8545 (OUTLIER) cc_final: 0.7923 (m-90) REVERT: C 375 SER cc_start: 0.8977 (t) cc_final: 0.8638 (p) REVERT: D 543 ASN cc_start: 0.9361 (m110) cc_final: 0.8997 (m-40) REVERT: D 579 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7997 (mtt-85) REVERT: D 590 GLN cc_start: 0.8160 (tp40) cc_final: 0.7724 (mt0) REVERT: D 626 MET cc_start: 0.7526 (tpp) cc_final: 0.7088 (ttt) REVERT: D 661 LEU cc_start: 0.9245 (tp) cc_final: 0.9015 (tp) REVERT: E 49 GLU cc_start: 0.8615 (pm20) cc_final: 0.8330 (mp0) REVERT: E 92 GLU cc_start: 0.8802 (tt0) cc_final: 0.8275 (tm-30) REVERT: E 150 MET cc_start: 0.7705 (mpp) cc_final: 0.7366 (mpp) REVERT: E 198 THR cc_start: 0.9296 (m) cc_final: 0.9093 (p) REVERT: E 227 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5975 (ttmm) REVERT: F 530 MET cc_start: 0.8905 (ttp) cc_final: 0.8613 (ttp) REVERT: F 550 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8351 (tm-30) REVERT: F 577 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8370 (tm-30) REVERT: F 621 GLU cc_start: 0.8857 (tt0) cc_final: 0.8161 (pt0) REVERT: F 648 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8931 (pp20) outliers start: 73 outliers final: 37 residues processed: 269 average time/residue: 0.5842 time to fit residues: 174.9290 Evaluate side-chains 221 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 617 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 128 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN D 577 GLN D 653 GLN E 99 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.085534 restraints weight = 35685.197| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 4.30 r_work: 0.3137 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16496 Z= 0.188 Angle : 0.732 13.775 22626 Z= 0.347 Chirality : 0.046 0.298 2871 Planarity : 0.004 0.042 2708 Dihedral : 7.192 72.755 4169 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 4.83 % Allowed : 19.33 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1687 helix: 1.85 (0.26), residues: 424 sheet: 0.42 (0.23), residues: 448 loop : -0.44 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 617 TYR 0.019 0.002 TYR B 638 PHE 0.016 0.002 PHE A 53 TRP 0.032 0.002 TRP A 69 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00430 (16359) covalent geometry : angle 0.68424 (22249) SS BOND : bond 0.00627 ( 34) SS BOND : angle 1.23432 ( 68) hydrogen bonds : bond 0.04812 ( 645) hydrogen bonds : angle 4.98574 ( 1740) link_ALPHA1-2 : bond 0.00683 ( 4) link_ALPHA1-2 : angle 2.47958 ( 12) link_ALPHA1-3 : bond 0.00958 ( 3) link_ALPHA1-3 : angle 1.75463 ( 9) link_ALPHA1-6 : bond 0.00715 ( 4) link_ALPHA1-6 : angle 1.98752 ( 12) link_BETA1-3 : bond 0.00557 ( 1) link_BETA1-3 : angle 2.15272 ( 3) link_BETA1-4 : bond 0.00400 ( 26) link_BETA1-4 : angle 1.79279 ( 78) link_NAG-ASN : bond 0.00403 ( 65) link_NAG-ASN : angle 2.47732 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 206 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.8034 (t0) cc_final: 0.7558 (t0) REVERT: A 161 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7556 (ttp) REVERT: A 360 ARG cc_start: 0.7867 (ttp-170) cc_final: 0.7198 (mtp85) REVERT: A 475 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6858 (mmt) REVERT: B 568 LEU cc_start: 0.8559 (tp) cc_final: 0.8351 (tt) REVERT: B 610 TRP cc_start: 0.8136 (t-100) cc_final: 0.7458 (t60) REVERT: B 622 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7831 (tt) REVERT: B 623 TRP cc_start: 0.5670 (OUTLIER) cc_final: 0.5358 (m-10) REVERT: B 633 LYS cc_start: 0.9419 (tttm) cc_final: 0.9162 (pttm) REVERT: C 151 ARG cc_start: 0.8124 (tpt170) cc_final: 0.7859 (tpt170) REVERT: C 161 MET cc_start: 0.8213 (tpp) cc_final: 0.7857 (tpt) REVERT: C 230 ASP cc_start: 0.9156 (t0) cc_final: 0.8733 (t70) REVERT: C 308 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7653 (tpp80) REVERT: C 375 SER cc_start: 0.9012 (t) cc_final: 0.8716 (p) REVERT: D 543 ASN cc_start: 0.9351 (m110) cc_final: 0.8972 (m-40) REVERT: D 579 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7899 (mtt-85) REVERT: D 590 GLN cc_start: 0.8269 (tp40) cc_final: 0.7926 (tt0) REVERT: D 657 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8473 (tt0) REVERT: D 659 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6718 (t0) REVERT: E 49 GLU cc_start: 0.8667 (pm20) cc_final: 0.8359 (mp0) REVERT: E 92 GLU cc_start: 0.8820 (tt0) cc_final: 0.8268 (tm-30) REVERT: E 123 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8317 (t) REVERT: E 150 MET cc_start: 0.7751 (mpp) cc_final: 0.7370 (mpp) REVERT: E 482 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8745 (mp0) REVERT: F 530 MET cc_start: 0.8851 (ttp) cc_final: 0.8567 (ttp) REVERT: F 550 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8294 (tm-30) REVERT: F 577 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8482 (tm-30) REVERT: F 621 GLU cc_start: 0.8792 (tt0) cc_final: 0.8212 (pt0) REVERT: F 648 GLU cc_start: 0.9285 (tm-30) cc_final: 0.8876 (pp20) REVERT: F 649 SER cc_start: 0.8173 (t) cc_final: 0.7868 (p) outliers start: 74 outliers final: 40 residues processed: 260 average time/residue: 0.6289 time to fit residues: 181.1265 Evaluate side-chains 228 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 482 GLU Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 49 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN C 328 GLN D 577 GLN D 653 GLN E 99 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.103569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083787 restraints weight = 35201.386| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 4.35 r_work: 0.3098 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16496 Z= 0.246 Angle : 0.794 13.216 22626 Z= 0.375 Chirality : 0.047 0.283 2871 Planarity : 0.004 0.043 2708 Dihedral : 7.404 68.371 4169 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 5.36 % Allowed : 19.33 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1687 helix: 1.70 (0.26), residues: 427 sheet: 0.29 (0.24), residues: 425 loop : -0.65 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 617 TYR 0.038 0.002 TYR B 638 PHE 0.019 0.002 PHE E 376 TRP 0.018 0.002 TRP D 610 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00567 (16359) covalent geometry : angle 0.74673 (22249) SS BOND : bond 0.00563 ( 34) SS BOND : angle 1.21455 ( 68) hydrogen bonds : bond 0.05061 ( 645) hydrogen bonds : angle 5.13392 ( 1740) link_ALPHA1-2 : bond 0.00577 ( 4) link_ALPHA1-2 : angle 2.59598 ( 12) link_ALPHA1-3 : bond 0.00845 ( 3) link_ALPHA1-3 : angle 1.90073 ( 9) link_ALPHA1-6 : bond 0.00737 ( 4) link_ALPHA1-6 : angle 1.90111 ( 12) link_BETA1-3 : bond 0.00573 ( 1) link_BETA1-3 : angle 2.06424 ( 3) link_BETA1-4 : bond 0.00420 ( 26) link_BETA1-4 : angle 1.78676 ( 78) link_NAG-ASN : bond 0.00507 ( 65) link_NAG-ASN : angle 2.63390 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 204 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8862 (t) cc_final: 0.8601 (p) REVERT: A 115 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.9077 (p) REVERT: A 161 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7553 (ttp) REVERT: A 360 ARG cc_start: 0.7820 (ttp-170) cc_final: 0.7146 (mtp85) REVERT: A 423 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 475 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6724 (mmt) REVERT: B 542 ARG cc_start: 0.8345 (ttp-170) cc_final: 0.8104 (mtp180) REVERT: B 623 TRP cc_start: 0.5624 (OUTLIER) cc_final: 0.5187 (m100) REVERT: B 633 LYS cc_start: 0.9352 (tttm) cc_final: 0.9041 (pttm) REVERT: C 150 MET cc_start: 0.8272 (mmm) cc_final: 0.8006 (mmm) REVERT: C 151 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7658 (tpt170) REVERT: C 161 MET cc_start: 0.8234 (tpp) cc_final: 0.7842 (tpt) REVERT: C 230 ASP cc_start: 0.9263 (t0) cc_final: 0.8845 (t70) REVERT: C 308 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7547 (tpp80) REVERT: C 328 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7915 (tp40) REVERT: C 375 SER cc_start: 0.9032 (t) cc_final: 0.8722 (p) REVERT: C 425 ASN cc_start: 0.8866 (p0) cc_final: 0.8243 (p0) REVERT: D 543 ASN cc_start: 0.9352 (m110) cc_final: 0.8953 (m-40) REVERT: D 590 GLN cc_start: 0.8278 (tp40) cc_final: 0.7889 (tt0) REVERT: E 49 GLU cc_start: 0.8676 (pm20) cc_final: 0.8349 (mp0) REVERT: E 92 GLU cc_start: 0.8861 (tt0) cc_final: 0.8361 (tm-30) REVERT: E 123 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8278 (t) REVERT: E 150 MET cc_start: 0.7714 (mpp) cc_final: 0.7209 (mpp) REVERT: E 192 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7630 (tpp80) REVERT: E 227 LYS cc_start: 0.6051 (OUTLIER) cc_final: 0.5794 (ttmm) REVERT: E 395 TRP cc_start: 0.8097 (m100) cc_final: 0.7755 (m100) REVERT: E 477 ASP cc_start: 0.8871 (m-30) cc_final: 0.8612 (m-30) REVERT: E 482 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8662 (mp0) REVERT: F 530 MET cc_start: 0.8975 (ttp) cc_final: 0.8678 (ttp) REVERT: F 550 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8259 (tm-30) REVERT: F 577 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8485 (tm-30) REVERT: F 648 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8907 (tm-30) outliers start: 82 outliers final: 42 residues processed: 267 average time/residue: 0.5912 time to fit residues: 175.5873 Evaluate side-chains 238 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 482 GLU Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 75 optimal weight: 0.0020 chunk 147 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 ASN C 130 GLN C 328 GLN D 577 GLN D 653 GLN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086483 restraints weight = 35235.858| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 4.31 r_work: 0.3155 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16496 Z= 0.133 Angle : 0.697 13.716 22626 Z= 0.331 Chirality : 0.045 0.287 2871 Planarity : 0.004 0.041 2708 Dihedral : 6.792 63.541 4169 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.19 % Favored : 97.75 % Rotamer: Outliers : 3.79 % Allowed : 21.55 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1687 helix: 1.85 (0.27), residues: 424 sheet: 0.32 (0.24), residues: 422 loop : -0.57 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 617 TYR 0.041 0.002 TYR E 173 PHE 0.015 0.002 PHE A 53 TRP 0.017 0.001 TRP D 610 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00299 (16359) covalent geometry : angle 0.65087 (22249) SS BOND : bond 0.00270 ( 34) SS BOND : angle 1.20465 ( 68) hydrogen bonds : bond 0.04350 ( 645) hydrogen bonds : angle 4.85713 ( 1740) link_ALPHA1-2 : bond 0.00730 ( 4) link_ALPHA1-2 : angle 2.49019 ( 12) link_ALPHA1-3 : bond 0.01158 ( 3) link_ALPHA1-3 : angle 1.82171 ( 9) link_ALPHA1-6 : bond 0.00943 ( 4) link_ALPHA1-6 : angle 1.87212 ( 12) link_BETA1-3 : bond 0.00536 ( 1) link_BETA1-3 : angle 1.75343 ( 3) link_BETA1-4 : bond 0.00404 ( 26) link_BETA1-4 : angle 1.67591 ( 78) link_NAG-ASN : bond 0.00347 ( 65) link_NAG-ASN : angle 2.36743 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 220 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7934 (t0) cc_final: 0.7428 (t0) REVERT: A 161 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7401 (ttp) REVERT: A 360 ARG cc_start: 0.7783 (ttp-170) cc_final: 0.7167 (mtp85) REVERT: A 475 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6493 (mmt) REVERT: B 623 TRP cc_start: 0.5401 (OUTLIER) cc_final: 0.5018 (m100) REVERT: B 633 LYS cc_start: 0.9307 (tttm) cc_final: 0.8985 (pttm) REVERT: B 657 GLU cc_start: 0.7811 (tp30) cc_final: 0.7371 (tm-30) REVERT: C 150 MET cc_start: 0.8194 (mmm) cc_final: 0.7814 (mpt) REVERT: C 161 MET cc_start: 0.8287 (tpp) cc_final: 0.7971 (tpt) REVERT: C 230 ASP cc_start: 0.9238 (t0) cc_final: 0.8849 (t70) REVERT: C 308 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7425 (tpp80) REVERT: C 316 TRP cc_start: 0.8409 (OUTLIER) cc_final: 0.7617 (m-90) REVERT: C 328 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7703 (tp40) REVERT: C 375 SER cc_start: 0.9067 (t) cc_final: 0.8763 (p) REVERT: C 426 MET cc_start: 0.8815 (mmm) cc_final: 0.8608 (mmm) REVERT: D 543 ASN cc_start: 0.9319 (m110) cc_final: 0.8899 (m-40) REVERT: D 590 GLN cc_start: 0.8270 (tp40) cc_final: 0.7922 (tt0) REVERT: D 625 ASN cc_start: 0.8045 (t0) cc_final: 0.7835 (t0) REVERT: D 648 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8596 (pt0) REVERT: E 49 GLU cc_start: 0.8624 (pm20) cc_final: 0.8294 (mp0) REVERT: E 92 GLU cc_start: 0.8800 (tt0) cc_final: 0.8221 (tm-30) REVERT: E 123 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8283 (t) REVERT: E 150 MET cc_start: 0.7461 (mpp) cc_final: 0.7063 (mpp) REVERT: E 192 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7574 (tpp80) REVERT: E 198 THR cc_start: 0.9189 (m) cc_final: 0.8946 (p) REVERT: E 227 LYS cc_start: 0.5787 (OUTLIER) cc_final: 0.5532 (ttmm) REVERT: E 477 ASP cc_start: 0.8847 (m-30) cc_final: 0.8554 (m-30) REVERT: E 482 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8687 (mp0) REVERT: F 530 MET cc_start: 0.8772 (ttp) cc_final: 0.8526 (ttp) REVERT: F 550 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8137 (tm-30) REVERT: F 577 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8256 (tm-30) REVERT: F 593 LEU cc_start: 0.8455 (mt) cc_final: 0.8204 (tt) REVERT: F 621 GLU cc_start: 0.8884 (tt0) cc_final: 0.8194 (pt0) REVERT: F 648 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8873 (tm-30) outliers start: 58 outliers final: 31 residues processed: 258 average time/residue: 0.5990 time to fit residues: 171.7148 Evaluate side-chains 235 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 482 GLU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 179 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 328 GLN D 577 GLN D 653 GLN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.105387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.085774 restraints weight = 35390.103| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 4.26 r_work: 0.3139 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16496 Z= 0.182 Angle : 0.740 13.371 22626 Z= 0.352 Chirality : 0.045 0.289 2871 Planarity : 0.004 0.055 2708 Dihedral : 6.718 61.480 4169 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.92 % Rotamer: Outliers : 3.98 % Allowed : 22.21 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1687 helix: 1.72 (0.27), residues: 427 sheet: 0.18 (0.24), residues: 435 loop : -0.61 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 469 TYR 0.027 0.002 TYR B 638 PHE 0.015 0.002 PHE E 159 TRP 0.018 0.002 TRP B 596 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00424 (16359) covalent geometry : angle 0.69481 (22249) SS BOND : bond 0.00399 ( 34) SS BOND : angle 1.66918 ( 68) hydrogen bonds : bond 0.04550 ( 645) hydrogen bonds : angle 4.88577 ( 1740) link_ALPHA1-2 : bond 0.00611 ( 4) link_ALPHA1-2 : angle 2.50800 ( 12) link_ALPHA1-3 : bond 0.00887 ( 3) link_ALPHA1-3 : angle 1.87275 ( 9) link_ALPHA1-6 : bond 0.00777 ( 4) link_ALPHA1-6 : angle 1.81971 ( 12) link_BETA1-3 : bond 0.00536 ( 1) link_BETA1-3 : angle 1.78257 ( 3) link_BETA1-4 : bond 0.00400 ( 26) link_BETA1-4 : angle 1.67456 ( 78) link_NAG-ASN : bond 0.00379 ( 65) link_NAG-ASN : angle 2.37336 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 198 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7488 (ttp) REVERT: A 173 TYR cc_start: 0.8654 (p90) cc_final: 0.8440 (p90) REVERT: A 351 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8696 (mptm) REVERT: A 360 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7211 (mtp85) REVERT: A 475 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6729 (mmt) REVERT: B 623 TRP cc_start: 0.5643 (OUTLIER) cc_final: 0.5272 (m100) REVERT: B 633 LYS cc_start: 0.9342 (tttm) cc_final: 0.9032 (pttm) REVERT: B 657 GLU cc_start: 0.7934 (tp30) cc_final: 0.7398 (tm-30) REVERT: C 150 MET cc_start: 0.8128 (mmm) cc_final: 0.7714 (mpt) REVERT: C 151 ARG cc_start: 0.7989 (tpt170) cc_final: 0.7703 (tpt170) REVERT: C 161 MET cc_start: 0.8358 (tpp) cc_final: 0.7996 (tpt) REVERT: C 230 ASP cc_start: 0.9275 (t0) cc_final: 0.8863 (t70) REVERT: C 308 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7576 (tpp80) REVERT: C 328 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7512 (tp40) REVERT: C 375 SER cc_start: 0.9079 (t) cc_final: 0.8756 (p) REVERT: D 543 ASN cc_start: 0.9356 (m110) cc_final: 0.8954 (m-40) REVERT: D 590 GLN cc_start: 0.8341 (tp40) cc_final: 0.7938 (tt0) REVERT: E 49 GLU cc_start: 0.8704 (pm20) cc_final: 0.8370 (mp0) REVERT: E 92 GLU cc_start: 0.8878 (tt0) cc_final: 0.8412 (tm-30) REVERT: E 123 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8335 (t) REVERT: E 150 MET cc_start: 0.7580 (mpp) cc_final: 0.7176 (mpp) REVERT: E 227 LYS cc_start: 0.5975 (OUTLIER) cc_final: 0.5688 (ttmm) REVERT: E 477 ASP cc_start: 0.8863 (m-30) cc_final: 0.8577 (m-30) REVERT: E 482 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8698 (mp0) REVERT: F 530 MET cc_start: 0.8816 (ttp) cc_final: 0.8428 (ttp) REVERT: F 550 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8248 (tm-30) REVERT: F 577 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8380 (tm-30) REVERT: F 621 GLU cc_start: 0.8901 (tt0) cc_final: 0.8244 (pt0) REVERT: F 648 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8870 (tm-30) outliers start: 61 outliers final: 34 residues processed: 242 average time/residue: 0.5936 time to fit residues: 159.9104 Evaluate side-chains 231 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 482 GLU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 649 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 164 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 328 GLN D 653 GLN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085348 restraints weight = 35385.830| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 4.30 r_work: 0.3137 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16496 Z= 0.176 Angle : 0.732 14.249 22626 Z= 0.349 Chirality : 0.045 0.290 2871 Planarity : 0.004 0.045 2708 Dihedral : 6.500 59.754 4169 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 3.66 % Allowed : 22.66 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.20), residues: 1687 helix: 1.66 (0.27), residues: 427 sheet: 0.19 (0.24), residues: 424 loop : -0.65 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 469 TYR 0.035 0.002 TYR F 643 PHE 0.016 0.002 PHE A 53 TRP 0.018 0.001 TRP D 610 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00410 (16359) covalent geometry : angle 0.69019 (22249) SS BOND : bond 0.00327 ( 34) SS BOND : angle 1.22778 ( 68) hydrogen bonds : bond 0.04517 ( 645) hydrogen bonds : angle 4.88726 ( 1740) link_ALPHA1-2 : bond 0.00610 ( 4) link_ALPHA1-2 : angle 2.50264 ( 12) link_ALPHA1-3 : bond 0.00888 ( 3) link_ALPHA1-3 : angle 1.84703 ( 9) link_ALPHA1-6 : bond 0.00790 ( 4) link_ALPHA1-6 : angle 1.65778 ( 12) link_BETA1-3 : bond 0.00515 ( 1) link_BETA1-3 : angle 1.72224 ( 3) link_BETA1-4 : bond 0.00404 ( 26) link_BETA1-4 : angle 1.66599 ( 78) link_NAG-ASN : bond 0.00376 ( 65) link_NAG-ASN : angle 2.32731 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8726 (mptm) REVERT: A 360 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.7255 (mtp85) REVERT: A 475 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6797 (mmt) REVERT: B 623 TRP cc_start: 0.5736 (OUTLIER) cc_final: 0.5354 (m100) REVERT: B 633 LYS cc_start: 0.9327 (tttm) cc_final: 0.9024 (pttm) REVERT: B 657 GLU cc_start: 0.7994 (tp30) cc_final: 0.7591 (tm-30) REVERT: B 661 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7520 (tm) REVERT: C 150 MET cc_start: 0.8188 (mmm) cc_final: 0.7957 (mpt) REVERT: C 151 ARG cc_start: 0.7990 (tpt170) cc_final: 0.7713 (tpt170) REVERT: C 161 MET cc_start: 0.8383 (tpp) cc_final: 0.8037 (tpt) REVERT: C 230 ASP cc_start: 0.9290 (t0) cc_final: 0.8875 (t70) REVERT: C 308 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7640 (tpp80) REVERT: C 328 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7755 (tp40) REVERT: C 375 SER cc_start: 0.9019 (t) cc_final: 0.8723 (p) REVERT: C 425 ASN cc_start: 0.8802 (p0) cc_final: 0.8437 (p0) REVERT: D 543 ASN cc_start: 0.9389 (m110) cc_final: 0.8968 (m-40) REVERT: D 579 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7804 (mtt-85) REVERT: D 590 GLN cc_start: 0.8351 (tp40) cc_final: 0.7952 (tt0) REVERT: D 648 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8560 (pt0) REVERT: E 49 GLU cc_start: 0.8699 (pm20) cc_final: 0.8380 (mp0) REVERT: E 92 GLU cc_start: 0.8943 (tt0) cc_final: 0.8464 (tm-30) REVERT: E 150 MET cc_start: 0.7585 (mpp) cc_final: 0.7226 (mpp) REVERT: E 227 LYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5853 (ttmm) REVERT: E 477 ASP cc_start: 0.8825 (m-30) cc_final: 0.8523 (m-30) REVERT: F 550 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8289 (tm-30) REVERT: F 577 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8411 (tm-30) REVERT: F 621 GLU cc_start: 0.8922 (tt0) cc_final: 0.8281 (pt0) REVERT: F 648 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8871 (tm-30) outliers start: 56 outliers final: 33 residues processed: 241 average time/residue: 0.5746 time to fit residues: 153.9486 Evaluate side-chains 234 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 579 ARG Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 649 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 122 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 161 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN D 653 GLN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** 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 = 0.3584 r_free = 0.3584 target = 0.105907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086332 restraints weight = 35332.923| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 4.28 r_work: 0.3154 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16496 Z= 0.160 Angle : 0.731 14.585 22626 Z= 0.348 Chirality : 0.045 0.291 2871 Planarity : 0.004 0.042 2708 Dihedral : 6.318 57.144 4169 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 3.33 % Allowed : 23.12 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1687 helix: 1.59 (0.26), residues: 430 sheet: 0.12 (0.23), residues: 444 loop : -0.72 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 469 TYR 0.034 0.002 TYR C 484 PHE 0.018 0.002 PHE E 159 TRP 0.019 0.001 TRP D 610 HIS 0.005 0.001 HIS F 564 Details of bonding type rmsd covalent geometry : bond 0.00374 (16359) covalent geometry : angle 0.69146 (22249) SS BOND : bond 0.00314 ( 34) SS BOND : angle 1.13026 ( 68) hydrogen bonds : bond 0.04427 ( 645) hydrogen bonds : angle 4.87805 ( 1740) link_ALPHA1-2 : bond 0.00632 ( 4) link_ALPHA1-2 : angle 2.43733 ( 12) link_ALPHA1-3 : bond 0.00907 ( 3) link_ALPHA1-3 : angle 1.79794 ( 9) link_ALPHA1-6 : bond 0.00743 ( 4) link_ALPHA1-6 : angle 1.62446 ( 12) link_BETA1-3 : bond 0.00505 ( 1) link_BETA1-3 : angle 1.69433 ( 3) link_BETA1-4 : bond 0.00407 ( 26) link_BETA1-4 : angle 1.64499 ( 78) link_NAG-ASN : bond 0.00366 ( 65) link_NAG-ASN : angle 2.27277 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 ARG cc_start: 0.7825 (ttp-170) cc_final: 0.7198 (mtp85) REVERT: A 475 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6647 (mmt) REVERT: B 623 TRP cc_start: 0.5617 (OUTLIER) cc_final: 0.5248 (m100) REVERT: B 633 LYS cc_start: 0.9272 (tttm) cc_final: 0.8957 (pttm) REVERT: B 657 GLU cc_start: 0.7891 (tp30) cc_final: 0.7522 (tm-30) REVERT: B 661 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7467 (tm) REVERT: C 150 MET cc_start: 0.8120 (mmm) cc_final: 0.7882 (mpt) REVERT: C 151 ARG cc_start: 0.7966 (tpt170) cc_final: 0.7704 (tpt170) REVERT: C 161 MET cc_start: 0.8308 (tpp) cc_final: 0.7982 (tpt) REVERT: C 230 ASP cc_start: 0.9275 (t0) cc_final: 0.8867 (t70) REVERT: C 308 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7523 (tpp80) REVERT: C 328 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7516 (tp40) REVERT: C 375 SER cc_start: 0.8993 (t) cc_final: 0.8676 (p) REVERT: C 425 ASN cc_start: 0.8797 (p0) cc_final: 0.8430 (p0) REVERT: D 543 ASN cc_start: 0.9357 (m110) cc_final: 0.8924 (m-40) REVERT: D 590 GLN cc_start: 0.8353 (tp40) cc_final: 0.7924 (tt0) REVERT: E 49 GLU cc_start: 0.8670 (pm20) cc_final: 0.8345 (mp0) REVERT: E 92 GLU cc_start: 0.8935 (tt0) cc_final: 0.8392 (tm-30) REVERT: E 150 MET cc_start: 0.7540 (mpp) cc_final: 0.7248 (mpp) REVERT: E 227 LYS cc_start: 0.5928 (OUTLIER) cc_final: 0.5643 (ttmm) REVERT: E 477 ASP cc_start: 0.8793 (m-30) cc_final: 0.8480 (m-30) REVERT: F 550 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8202 (tm-30) REVERT: F 577 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8282 (tm-30) REVERT: F 621 GLU cc_start: 0.8918 (tt0) cc_final: 0.8263 (pt0) REVERT: F 648 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8833 (tm-30) outliers start: 51 outliers final: 32 residues processed: 239 average time/residue: 0.5705 time to fit residues: 151.6130 Evaluate side-chains 229 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 623 TRP Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 649 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 124 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 169 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 0.0570 chunk 56 optimal weight: 0.7980 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 328 GLN D 653 GLN E 99 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.086190 restraints weight = 35099.552| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 4.26 r_work: 0.3150 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16496 Z= 0.164 Angle : 0.728 14.543 22626 Z= 0.348 Chirality : 0.045 0.289 2871 Planarity : 0.004 0.041 2708 Dihedral : 6.206 55.058 4169 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.04 % Rotamer: Outliers : 3.00 % Allowed : 23.38 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.20), residues: 1687 helix: 1.74 (0.27), residues: 418 sheet: 0.08 (0.23), residues: 444 loop : -0.66 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 469 TYR 0.028 0.002 TYR F 643 PHE 0.017 0.002 PHE E 159 TRP 0.019 0.001 TRP B 596 HIS 0.005 0.001 HIS F 564 Details of bonding type rmsd covalent geometry : bond 0.00382 (16359) covalent geometry : angle 0.68975 (22249) SS BOND : bond 0.00311 ( 34) SS BOND : angle 1.06451 ( 68) hydrogen bonds : bond 0.04401 ( 645) hydrogen bonds : angle 4.87381 ( 1740) link_ALPHA1-2 : bond 0.00618 ( 4) link_ALPHA1-2 : angle 2.41743 ( 12) link_ALPHA1-3 : bond 0.00877 ( 3) link_ALPHA1-3 : angle 1.81803 ( 9) link_ALPHA1-6 : bond 0.00759 ( 4) link_ALPHA1-6 : angle 1.65788 ( 12) link_BETA1-3 : bond 0.00497 ( 1) link_BETA1-3 : angle 1.67692 ( 3) link_BETA1-4 : bond 0.00406 ( 26) link_BETA1-4 : angle 1.63943 ( 78) link_NAG-ASN : bond 0.00358 ( 65) link_NAG-ASN : angle 2.24765 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5042.53 seconds wall clock time: 86 minutes 56.68 seconds (5216.68 seconds total)