Starting phenix.real_space_refine on Wed Mar 4 17:41:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l7u_23219/03_2026/7l7u_23219.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l7u_23219/03_2026/7l7u_23219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l7u_23219/03_2026/7l7u_23219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l7u_23219/03_2026/7l7u_23219.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l7u_23219/03_2026/7l7u_23219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l7u_23219/03_2026/7l7u_23219.map" } resolution = 3.8 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= 0.002 sd= 0.010 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 105 5.16 5 C 9504 2.51 5 N 2544 2.21 5 O 3105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 15258 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3491 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "B" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1156 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3491 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "D" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1156 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3491 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 20, 'TRANS': 421} Chain breaks: 3 Chain: "F" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1156 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" 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: 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.81, per 1000 atoms: 0.25 Number of scatterers: 15258 At special positions: 0 Unit cell: (128.8, 125.35, 118.45, 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 105 16.00 O 3105 8.00 N 2544 7.00 C 9504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, 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=2.10 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=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 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 378 " - pdb=" SG CYS C 445 " distance=2.03 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=2.09 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA O 3 " - " MAN O 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA O 3 " - " MAN O 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 276 " " NAG A 603 " - " ASN A 386 " " NAG A 604 " - " ASN A 363 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 133 " " NAG A 607 " - " ASN A 241 " " NAG A 608 " - " ASN A 289 " " NAG A 609 " - " ASN A 339 " " NAG A 610 " - " ASN A 355 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 276 " " NAG C 603 " - " ASN C 386 " " NAG C 604 " - " ASN C 363 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 133 " " NAG C 607 " - " ASN C 241 " " NAG C 608 " - " ASN C 289 " " NAG C 609 " - " ASN C 339 " " NAG C 610 " - " ASN C 355 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 160 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 386 " " NAG E 604 " - " ASN E 363 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 133 " " NAG E 607 " - " ASN E 241 " " NAG E 608 " - " ASN E 289 " " NAG E 609 " - " ASN E 339 " " NAG E 610 " - " ASN E 355 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 448 " " NAG I 1 " - " ASN A 295 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 156 " " NAG L 1 " - " ASN A 301 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN C 262 " " NAG P 1 " - " ASN C 448 " " NAG Q 1 " - " ASN C 295 " " NAG R 1 " - " ASN C 197 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 301 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 448 " " NAG Y 1 " - " ASN E 295 " " NAG Z 1 " - " ASN E 197 " " NAG a 1 " - " ASN E 156 " " NAG b 1 " - " ASN E 301 " " NAG c 1 " - " ASN E 88 " " NAG d 1 " - " ASN E 332 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 673.7 milliseconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 27 sheets defined 31.2% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.684A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.021A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.827A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.582A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 542 through 556 Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.684A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.022A 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 387 through 392 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.827A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.582A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (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 542 through 556 Processing helix chain 'D' and resid 560 through 568 Processing helix chain 'D' and resid 568 through 596 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 663 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.684A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.021A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.826A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.582A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 542 through 556 Processing helix chain 'F' and resid 560 through 568 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.911A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (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 53 through 55 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 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.245A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.531A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 10.951A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 312 removed outlier: 6.563A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY A 321 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.911A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.245A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.531A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 10.951A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.836A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 312 removed outlier: 6.562A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY C 321 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.910A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.245A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.531A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 removed outlier: 10.951A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.835A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.969A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.913A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 301 through 312 removed outlier: 6.563A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3638 1.32 - 1.46: 4661 1.46 - 1.59: 7065 1.59 - 1.73: 50 1.73 - 1.86: 126 Bond restraints: 15540 Sorted by residual: bond pdb=" CB LEU B 520 " pdb=" CG LEU B 520 " ideal model delta sigma weight residual 1.530 1.640 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" CB LEU D 520 " pdb=" CG LEU D 520 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CB LEU F 520 " pdb=" CG LEU F 520 " ideal model delta sigma weight residual 1.530 1.639 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CB PHE A 376 " pdb=" CG PHE A 376 " ideal model delta sigma weight residual 1.502 1.379 0.123 2.30e-02 1.89e+03 2.85e+01 bond pdb=" CB PHE E 376 " pdb=" CG PHE E 376 " ideal model delta sigma weight residual 1.502 1.380 0.122 2.30e-02 1.89e+03 2.83e+01 ... (remaining 15535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 17633 2.21 - 4.42: 2984 4.42 - 6.63: 438 6.63 - 8.85: 44 8.85 - 11.06: 3 Bond angle restraints: 21102 Sorted by residual: angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 128.14 -8.27 1.04e+00 9.25e-01 6.32e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 128.12 -8.25 1.04e+00 9.25e-01 6.30e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.87 128.11 -8.24 1.04e+00 9.25e-01 6.28e+01 angle pdb=" C GLY E 237 " pdb=" N PRO E 238 " pdb=" CA PRO E 238 " ideal model delta sigma weight residual 119.76 127.28 -7.52 1.03e+00 9.43e-01 5.33e+01 angle pdb=" C GLY A 237 " pdb=" N PRO A 238 " pdb=" CA PRO A 238 " ideal model delta sigma weight residual 119.76 127.25 -7.49 1.03e+00 9.43e-01 5.29e+01 ... (remaining 21097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 10206 21.10 - 42.20: 238 42.20 - 63.30: 71 63.30 - 84.40: 42 84.40 - 105.50: 15 Dihedral angle restraints: 10572 sinusoidal: 5481 harmonic: 5091 Sorted by residual: 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 93.00 161.68 -68.68 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 161.67 -68.67 1 1.00e+01 1.00e-02 6.11e+01 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 93.00 161.67 -68.67 1 1.00e+01 1.00e-02 6.11e+01 ... (remaining 10569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1799 0.111 - 0.221: 523 0.221 - 0.332: 210 0.332 - 0.442: 105 0.442 - 0.553: 27 Chirality restraints: 2664 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 ... (remaining 2661 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " -0.349 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG A 607 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 607 " 0.349 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG C 607 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG C 607 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG C 607 " -0.531 2.00e-02 2.50e+03 pdb=" O7 NAG C 607 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 607 " -0.348 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG E 607 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG E 607 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG E 607 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG E 607 " -0.121 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6283 2.91 - 3.41: 13691 3.41 - 3.90: 25725 3.90 - 4.40: 28847 4.40 - 4.90: 45643 Nonbonded interactions: 120189 Sorted by model distance: nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.411 2.496 nonbonded pdb=" N ILE C 213 " pdb=" O ILE C 213 " model vdw 2.412 2.496 nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.412 2.496 nonbonded pdb=" O3 NAG G 1 " pdb=" O7 NAG G 1 " model vdw 2.432 3.040 nonbonded pdb=" O3 NAG W 1 " pdb=" O7 NAG W 1 " model vdw 2.432 3.040 ... (remaining 120184 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'O' selection = chain 'W' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.390 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.023 0.136 15660 Z= 1.217 Angle : 1.716 11.057 21438 Z= 1.096 Chirality : 0.149 0.553 2664 Planarity : 0.019 0.299 2565 Dihedral : 11.592 105.496 7200 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.18 % 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: 0.66 (0.19), residues: 1731 helix: -0.11 (0.21), residues: 480 sheet: 1.31 (0.22), residues: 495 loop : 0.37 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 480 TYR 0.030 0.007 TYR E 217 PHE 0.019 0.006 PHE A 93 TRP 0.068 0.013 TRP E 479 HIS 0.008 0.003 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.02266 (15540) covalent geometry : angle 1.68450 (21102) SS BOND : bond 0.02346 ( 24) SS BOND : angle 3.50680 ( 48) hydrogen bonds : bond 0.17892 ( 630) hydrogen bonds : angle 7.08243 ( 1809) link_ALPHA1-3 : bond 0.00181 ( 3) link_ALPHA1-3 : angle 0.79878 ( 9) link_ALPHA1-6 : bond 0.00015 ( 3) link_ALPHA1-6 : angle 0.41145 ( 9) link_BETA1-4 : bond 0.06374 ( 27) link_BETA1-4 : angle 4.13692 ( 81) link_NAG-ASN : bond 0.07213 ( 63) link_NAG-ASN : angle 2.60483 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8354 (mtp) cc_final: 0.8024 (mtp) REVERT: A 140 ASP cc_start: 0.7871 (t0) cc_final: 0.7420 (t0) REVERT: A 179 LEU cc_start: 0.9376 (mt) cc_final: 0.9172 (mt) REVERT: B 523 LEU cc_start: 0.9331 (mt) cc_final: 0.8967 (mt) REVERT: B 534 SER cc_start: 0.8676 (p) cc_final: 0.8343 (p) REVERT: B 543 ASN cc_start: 0.8985 (t0) cc_final: 0.8478 (t0) REVERT: B 564 HIS cc_start: 0.5295 (t70) cc_final: 0.4893 (t-90) REVERT: B 577 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8182 (tt0) REVERT: B 616 ASN cc_start: 0.8382 (p0) cc_final: 0.8160 (p0) REVERT: B 617 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7548 (ttp80) REVERT: B 647 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6714 (mt-10) REVERT: C 100 MET cc_start: 0.8542 (mtp) cc_final: 0.8030 (mtp) REVERT: C 115 SER cc_start: 0.9087 (m) cc_final: 0.8812 (t) REVERT: C 125 LEU cc_start: 0.8791 (tt) cc_final: 0.8519 (tt) REVERT: D 577 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8182 (tt0) REVERT: D 627 THR cc_start: 0.8270 (p) cc_final: 0.8009 (p) REVERT: E 140 ASP cc_start: 0.7997 (t0) cc_final: 0.7782 (t0) REVERT: F 523 LEU cc_start: 0.9292 (mt) cc_final: 0.8888 (mt) REVERT: F 577 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8075 (tt0) REVERT: F 617 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7777 (tpp80) REVERT: F 637 ASN cc_start: 0.7057 (m-40) cc_final: 0.6855 (m-40) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.1293 time to fit residues: 83.7367 Evaluate side-chains 236 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 103 GLN A 130 GLN A 258 GLN A 302 ASN B 550 GLN B 562 GLN C 85 HIS C 103 GLN C 114 GLN C 130 GLN C 258 GLN C 302 ASN D 550 GLN D 562 GLN D 656 ASN E 85 HIS E 114 GLN E 258 GLN E 302 ASN E 478 ASN F 562 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111791 restraints weight = 21965.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114834 restraints weight = 15310.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116898 restraints weight = 11994.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118124 restraints weight = 10207.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119120 restraints weight = 9179.427| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15660 Z= 0.190 Angle : 0.749 11.050 21438 Z= 0.375 Chirality : 0.049 0.218 2664 Planarity : 0.004 0.056 2565 Dihedral : 9.146 80.774 3864 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.29 % Allowed : 8.44 % Favored : 89.27 % 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: 0.90 (0.20), residues: 1731 helix: 1.18 (0.24), residues: 471 sheet: 1.03 (0.24), residues: 459 loop : 0.08 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 350 TYR 0.011 0.002 TYR A 384 PHE 0.019 0.003 PHE E 468 TRP 0.025 0.002 TRP E 479 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00431 (15540) covalent geometry : angle 0.70752 (21102) SS BOND : bond 0.00886 ( 24) SS BOND : angle 1.26457 ( 48) hydrogen bonds : bond 0.06209 ( 630) hydrogen bonds : angle 5.56478 ( 1809) link_ALPHA1-3 : bond 0.01185 ( 3) link_ALPHA1-3 : angle 2.64872 ( 9) link_ALPHA1-6 : bond 0.00467 ( 3) link_ALPHA1-6 : angle 1.55636 ( 9) link_BETA1-4 : bond 0.00215 ( 27) link_BETA1-4 : angle 2.18006 ( 81) link_NAG-ASN : bond 0.00446 ( 63) link_NAG-ASN : angle 2.20556 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 263 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7904 (mtp) cc_final: 0.7684 (mtp) REVERT: B 523 LEU cc_start: 0.9264 (mt) cc_final: 0.8929 (mt) REVERT: B 535 MET cc_start: 0.7401 (mmm) cc_final: 0.7187 (mmp) REVERT: B 543 ASN cc_start: 0.8841 (t0) cc_final: 0.8456 (t0) REVERT: B 577 GLN cc_start: 0.7943 (tp-100) cc_final: 0.7529 (tt0) REVERT: B 615 SER cc_start: 0.8335 (t) cc_final: 0.8058 (m) REVERT: C 424 ILE cc_start: 0.9154 (mp) cc_final: 0.8937 (mt) REVERT: D 577 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7500 (tt0) REVERT: D 615 SER cc_start: 0.8301 (t) cc_final: 0.8095 (m) REVERT: D 616 ASN cc_start: 0.7892 (p0) cc_final: 0.7598 (p0) REVERT: D 626 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7357 (ttm) REVERT: D 659 ASP cc_start: 0.7491 (m-30) cc_final: 0.7265 (m-30) REVERT: E 100 MET cc_start: 0.7506 (mtm) cc_final: 0.7286 (mtm) REVERT: F 577 GLN cc_start: 0.8022 (tp-100) cc_final: 0.7532 (tt0) REVERT: F 615 SER cc_start: 0.8441 (t) cc_final: 0.8091 (m) REVERT: F 626 MET cc_start: 0.8090 (ttp) cc_final: 0.7693 (ttt) outliers start: 36 outliers final: 17 residues processed: 286 average time/residue: 0.1051 time to fit residues: 47.1691 Evaluate side-chains 210 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 553 SER Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 136 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN F 607 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103787 restraints weight = 22469.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106530 restraints weight = 15838.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108430 restraints weight = 12606.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109583 restraints weight = 10827.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110368 restraints weight = 9799.104| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15660 Z= 0.221 Angle : 0.702 10.059 21438 Z= 0.347 Chirality : 0.047 0.217 2664 Planarity : 0.004 0.059 2565 Dihedral : 8.450 72.727 3864 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.67 % Allowed : 10.67 % Favored : 86.67 % 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: 0.63 (0.19), residues: 1731 helix: 1.12 (0.24), residues: 471 sheet: 0.79 (0.23), residues: 456 loop : -0.13 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 469 TYR 0.018 0.002 TYR A 217 PHE 0.014 0.002 PHE C 376 TRP 0.014 0.002 TRP C 479 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00525 (15540) covalent geometry : angle 0.67465 (21102) SS BOND : bond 0.00528 ( 24) SS BOND : angle 1.00107 ( 48) hydrogen bonds : bond 0.05504 ( 630) hydrogen bonds : angle 5.31772 ( 1809) link_ALPHA1-3 : bond 0.01147 ( 3) link_ALPHA1-3 : angle 2.33330 ( 9) link_ALPHA1-6 : bond 0.00440 ( 3) link_ALPHA1-6 : angle 1.46254 ( 9) link_BETA1-4 : bond 0.00513 ( 27) link_BETA1-4 : angle 1.61880 ( 81) link_NAG-ASN : bond 0.00302 ( 63) link_NAG-ASN : angle 1.80848 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.6808 (ttm) REVERT: A 100 MET cc_start: 0.7726 (mtp) cc_final: 0.7457 (mtp) REVERT: B 543 ASN cc_start: 0.8928 (t0) cc_final: 0.8370 (t0) REVERT: B 577 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7657 (tt0) REVERT: B 615 SER cc_start: 0.8450 (t) cc_final: 0.8225 (m) REVERT: B 659 ASP cc_start: 0.7789 (m-30) cc_final: 0.7582 (m-30) REVERT: C 95 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6499 (ttm) REVERT: C 342 LEU cc_start: 0.9123 (tp) cc_final: 0.8904 (mt) REVERT: C 424 ILE cc_start: 0.9222 (mp) cc_final: 0.8979 (mt) REVERT: D 615 SER cc_start: 0.8351 (t) cc_final: 0.8116 (m) REVERT: D 616 ASN cc_start: 0.7837 (p0) cc_final: 0.7496 (p0) REVERT: E 95 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.6737 (ttm) REVERT: F 577 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7445 (tt0) REVERT: F 615 SER cc_start: 0.8518 (t) cc_final: 0.8202 (m) REVERT: F 616 ASN cc_start: 0.8096 (p0) cc_final: 0.7889 (p0) REVERT: F 617 ARG cc_start: 0.8310 (tpp80) cc_final: 0.8091 (tpp80) outliers start: 42 outliers final: 32 residues processed: 232 average time/residue: 0.1066 time to fit residues: 38.6568 Evaluate side-chains 208 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 155 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN C 82 GLN E 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102137 restraints weight = 22115.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104948 restraints weight = 15144.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106924 restraints weight = 11766.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108193 restraints weight = 9936.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109149 restraints weight = 8854.726| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15660 Z= 0.126 Angle : 0.619 9.680 21438 Z= 0.303 Chirality : 0.045 0.225 2664 Planarity : 0.003 0.035 2565 Dihedral : 7.656 64.574 3864 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.79 % Allowed : 11.24 % Favored : 85.97 % 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: 0.68 (0.19), residues: 1731 helix: 1.25 (0.25), residues: 480 sheet: 0.76 (0.22), residues: 474 loop : -0.16 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 617 TYR 0.008 0.001 TYR C 191 PHE 0.014 0.001 PHE C 53 TRP 0.010 0.001 TRP A 479 HIS 0.004 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00275 (15540) covalent geometry : angle 0.59442 (21102) SS BOND : bond 0.00218 ( 24) SS BOND : angle 0.65478 ( 48) hydrogen bonds : bond 0.04649 ( 630) hydrogen bonds : angle 5.07394 ( 1809) link_ALPHA1-3 : bond 0.01149 ( 3) link_ALPHA1-3 : angle 2.19751 ( 9) link_ALPHA1-6 : bond 0.00519 ( 3) link_ALPHA1-6 : angle 1.59768 ( 9) link_BETA1-4 : bond 0.00523 ( 27) link_BETA1-4 : angle 1.43265 ( 81) link_NAG-ASN : bond 0.00295 ( 63) link_NAG-ASN : angle 1.63427 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 196 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6665 (ttm) REVERT: A 100 MET cc_start: 0.7615 (mtp) cc_final: 0.7414 (mtp) REVERT: A 161 MET cc_start: 0.8785 (tpt) cc_final: 0.8247 (tpt) REVERT: B 523 LEU cc_start: 0.9313 (mt) cc_final: 0.9039 (mt) REVERT: B 542 ARG cc_start: 0.7826 (ptm160) cc_final: 0.7621 (ptm160) REVERT: B 543 ASN cc_start: 0.8881 (t0) cc_final: 0.8463 (t0) REVERT: B 615 SER cc_start: 0.8322 (t) cc_final: 0.8109 (m) REVERT: B 617 ARG cc_start: 0.7970 (tpp80) cc_final: 0.7055 (ttp80) REVERT: B 626 MET cc_start: 0.8323 (ttt) cc_final: 0.7539 (ttt) REVERT: B 632 ASP cc_start: 0.7722 (t0) cc_final: 0.7382 (t0) REVERT: C 95 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6574 (ttm) REVERT: C 424 ILE cc_start: 0.9145 (mp) cc_final: 0.8916 (mt) REVERT: D 523 LEU cc_start: 0.9228 (mt) cc_final: 0.8949 (mt) REVERT: D 564 HIS cc_start: 0.5072 (t-90) cc_final: 0.4565 (t-90) REVERT: D 574 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7576 (mmtp) REVERT: D 615 SER cc_start: 0.8253 (t) cc_final: 0.7945 (m) REVERT: F 523 LEU cc_start: 0.9313 (mt) cc_final: 0.8908 (mt) REVERT: F 577 GLN cc_start: 0.7802 (tp-100) cc_final: 0.7533 (tt0) REVERT: F 615 SER cc_start: 0.8503 (t) cc_final: 0.8207 (m) REVERT: F 616 ASN cc_start: 0.8139 (p0) cc_final: 0.7794 (p0) outliers start: 44 outliers final: 25 residues processed: 221 average time/residue: 0.0970 time to fit residues: 34.5118 Evaluate side-chains 197 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 132 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 170 GLN E 114 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099933 restraints weight = 22775.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102666 restraints weight = 16072.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104547 restraints weight = 12758.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105771 restraints weight = 10951.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106654 restraints weight = 9900.547| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15660 Z= 0.196 Angle : 0.659 9.973 21438 Z= 0.320 Chirality : 0.047 0.238 2664 Planarity : 0.004 0.039 2565 Dihedral : 7.124 53.211 3864 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.56 % Allowed : 11.62 % Favored : 84.83 % 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: 0.39 (0.19), residues: 1731 helix: 1.12 (0.25), residues: 486 sheet: 0.60 (0.22), residues: 474 loop : -0.45 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 617 TYR 0.018 0.002 TYR A 217 PHE 0.014 0.002 PHE C 376 TRP 0.016 0.001 TRP E 96 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00467 (15540) covalent geometry : angle 0.63467 (21102) SS BOND : bond 0.00330 ( 24) SS BOND : angle 0.79440 ( 48) hydrogen bonds : bond 0.04695 ( 630) hydrogen bonds : angle 5.05441 ( 1809) link_ALPHA1-3 : bond 0.01211 ( 3) link_ALPHA1-3 : angle 2.45634 ( 9) link_ALPHA1-6 : bond 0.00449 ( 3) link_ALPHA1-6 : angle 1.34479 ( 9) link_BETA1-4 : bond 0.00422 ( 27) link_BETA1-4 : angle 1.40105 ( 81) link_NAG-ASN : bond 0.00207 ( 63) link_NAG-ASN : angle 1.68441 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.558 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: symmetry clash REVERT: A 95 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7151 (ttm) REVERT: B 615 SER cc_start: 0.8238 (t) cc_final: 0.8003 (m) REVERT: B 617 ARG cc_start: 0.8002 (tpp80) cc_final: 0.7319 (ttp80) REVERT: B 626 MET cc_start: 0.8133 (ttt) cc_final: 0.7137 (ttt) REVERT: C 95 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6766 (ttm) REVERT: C 424 ILE cc_start: 0.9210 (mp) cc_final: 0.8952 (mt) REVERT: D 530 MET cc_start: 0.8736 (mmm) cc_final: 0.8353 (mtp) REVERT: D 564 HIS cc_start: 0.5143 (t-90) cc_final: 0.4690 (t-90) REVERT: D 574 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7688 (mmtp) REVERT: D 615 SER cc_start: 0.8161 (t) cc_final: 0.7899 (m) REVERT: F 577 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7581 (tt0) REVERT: F 615 SER cc_start: 0.8446 (t) cc_final: 0.8195 (m) REVERT: F 616 ASN cc_start: 0.8207 (p0) cc_final: 0.7804 (p0) outliers start: 56 outliers final: 36 residues processed: 229 average time/residue: 0.1049 time to fit residues: 37.7230 Evaluate side-chains 216 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 130 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 66 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.101165 restraints weight = 22388.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.103933 restraints weight = 15296.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105789 restraints weight = 11899.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107058 restraints weight = 10052.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108030 restraints weight = 8965.324| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.003 0.032 15660 Z= 0.119 Angle : 0.590 9.606 21438 Z= 0.285 Chirality : 0.045 0.241 2664 Planarity : 0.003 0.039 2565 Dihedral : 6.534 58.742 3864 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.98 % Allowed : 12.63 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.19), residues: 1731 helix: 1.25 (0.25), residues: 486 sheet: 0.65 (0.22), residues: 468 loop : -0.41 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 617 TYR 0.008 0.001 TYR A 191 PHE 0.014 0.001 PHE C 53 TRP 0.014 0.001 TRP E 96 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00266 (15540) covalent geometry : angle 0.56774 (21102) SS BOND : bond 0.00198 ( 24) SS BOND : angle 0.59916 ( 48) hydrogen bonds : bond 0.04140 ( 630) hydrogen bonds : angle 4.90957 ( 1809) link_ALPHA1-3 : bond 0.01191 ( 3) link_ALPHA1-3 : angle 1.97110 ( 9) link_ALPHA1-6 : bond 0.00302 ( 3) link_ALPHA1-6 : angle 1.51214 ( 9) link_BETA1-4 : bond 0.00501 ( 27) link_BETA1-4 : angle 1.31039 ( 81) link_NAG-ASN : bond 0.00186 ( 63) link_NAG-ASN : angle 1.54626 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.552 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: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6808 (ttm) REVERT: A 161 MET cc_start: 0.8709 (tpt) cc_final: 0.8109 (tpt) REVERT: B 523 LEU cc_start: 0.9363 (mt) cc_final: 0.9008 (mt) REVERT: B 617 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7460 (ttp80) REVERT: B 626 MET cc_start: 0.8195 (ttt) cc_final: 0.6996 (ttt) REVERT: B 653 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 95 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6647 (ttm) REVERT: C 424 ILE cc_start: 0.9155 (mp) cc_final: 0.8927 (mt) REVERT: D 523 LEU cc_start: 0.9313 (mt) cc_final: 0.9032 (mt) REVERT: D 530 MET cc_start: 0.8713 (mmm) cc_final: 0.8130 (mtp) REVERT: D 564 HIS cc_start: 0.5080 (t-90) cc_final: 0.4555 (t70) REVERT: D 574 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7623 (mmtp) REVERT: E 150 MET cc_start: 0.8845 (mtp) cc_final: 0.8574 (mtp) REVERT: E 161 MET cc_start: 0.8537 (tpp) cc_final: 0.8269 (tpp) REVERT: E 195 ASN cc_start: 0.8182 (p0) cc_final: 0.7940 (p0) REVERT: F 523 LEU cc_start: 0.9344 (mt) cc_final: 0.9003 (mt) REVERT: F 530 MET cc_start: 0.8627 (mmm) cc_final: 0.8346 (mtp) REVERT: F 615 SER cc_start: 0.8458 (t) cc_final: 0.8226 (m) REVERT: F 616 ASN cc_start: 0.8131 (p0) cc_final: 0.7708 (p0) REVERT: F 617 ARG cc_start: 0.8045 (tpp80) cc_final: 0.7722 (tpp80) outliers start: 47 outliers final: 28 residues processed: 231 average time/residue: 0.1030 time to fit residues: 37.5115 Evaluate side-chains 204 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 161 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 55 optimal weight: 0.3980 chunk 127 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN E 328 GLN F 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102196 restraints weight = 22112.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104981 restraints weight = 15169.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106894 restraints weight = 11781.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108175 restraints weight = 9969.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109029 restraints weight = 8868.713| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15660 Z= 0.116 Angle : 0.599 12.373 21438 Z= 0.285 Chirality : 0.045 0.243 2664 Planarity : 0.003 0.035 2565 Dihedral : 6.100 54.374 3864 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.48 % Allowed : 13.40 % Favored : 84.13 % 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: 0.49 (0.19), residues: 1731 helix: 1.21 (0.25), residues: 486 sheet: 0.56 (0.21), residues: 498 loop : -0.35 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 542 TYR 0.023 0.001 TYR C 191 PHE 0.013 0.001 PHE C 53 TRP 0.035 0.001 TRP B 631 HIS 0.002 0.001 HIS F 564 Details of bonding type rmsd covalent geometry : bond 0.00259 (15540) covalent geometry : angle 0.57662 (21102) SS BOND : bond 0.00208 ( 24) SS BOND : angle 0.61208 ( 48) hydrogen bonds : bond 0.04032 ( 630) hydrogen bonds : angle 4.80603 ( 1809) link_ALPHA1-3 : bond 0.01247 ( 3) link_ALPHA1-3 : angle 1.79817 ( 9) link_ALPHA1-6 : bond 0.00197 ( 3) link_ALPHA1-6 : angle 1.71528 ( 9) link_BETA1-4 : bond 0.00500 ( 27) link_BETA1-4 : angle 1.27456 ( 81) link_NAG-ASN : bond 0.00327 ( 63) link_NAG-ASN : angle 1.57816 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.485 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: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6765 (ttm) REVERT: B 523 LEU cc_start: 0.9345 (mt) cc_final: 0.8998 (mt) REVERT: B 574 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7472 (mmtp) REVERT: B 653 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 424 ILE cc_start: 0.9169 (mp) cc_final: 0.8913 (mt) REVERT: D 523 LEU cc_start: 0.9309 (mt) cc_final: 0.9022 (mt) REVERT: D 530 MET cc_start: 0.8685 (mmm) cc_final: 0.8147 (mtp) REVERT: D 564 HIS cc_start: 0.4838 (t-90) cc_final: 0.4490 (t-90) REVERT: D 574 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7588 (mmtp) REVERT: E 150 MET cc_start: 0.8819 (mtp) cc_final: 0.8558 (mtp) REVERT: E 195 ASN cc_start: 0.8151 (p0) cc_final: 0.7924 (p0) REVERT: F 523 LEU cc_start: 0.9325 (mt) cc_final: 0.9010 (mt) REVERT: F 530 MET cc_start: 0.8610 (mmm) cc_final: 0.8387 (mtp) REVERT: F 540 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: F 615 SER cc_start: 0.8473 (t) cc_final: 0.8199 (m) REVERT: F 616 ASN cc_start: 0.8005 (p0) cc_final: 0.7537 (p0) REVERT: F 617 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7689 (tpp80) outliers start: 39 outliers final: 29 residues processed: 218 average time/residue: 0.0990 time to fit residues: 34.6745 Evaluate side-chains 207 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 23 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 153 optimal weight: 0.0070 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 170 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101976 restraints weight = 22521.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104764 restraints weight = 15275.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106747 restraints weight = 11840.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107950 restraints weight = 10012.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108654 restraints weight = 8960.063| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15660 Z= 0.120 Angle : 0.583 10.627 21438 Z= 0.282 Chirality : 0.044 0.246 2664 Planarity : 0.003 0.034 2565 Dihedral : 5.815 54.499 3864 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.73 % Allowed : 13.27 % Favored : 84.00 % 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: 0.50 (0.20), residues: 1731 helix: 1.28 (0.25), residues: 483 sheet: 0.56 (0.21), residues: 498 loop : -0.39 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.016 0.001 TYR C 191 PHE 0.012 0.001 PHE A 468 TRP 0.022 0.001 TRP E 96 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00272 (15540) covalent geometry : angle 0.56029 (21102) SS BOND : bond 0.00359 ( 24) SS BOND : angle 0.87224 ( 48) hydrogen bonds : bond 0.03937 ( 630) hydrogen bonds : angle 4.75657 ( 1809) link_ALPHA1-3 : bond 0.01184 ( 3) link_ALPHA1-3 : angle 1.55070 ( 9) link_ALPHA1-6 : bond 0.00138 ( 3) link_ALPHA1-6 : angle 1.69691 ( 9) link_BETA1-4 : bond 0.00478 ( 27) link_BETA1-4 : angle 1.24963 ( 81) link_NAG-ASN : bond 0.00232 ( 63) link_NAG-ASN : angle 1.52676 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.633 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: A 95 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6733 (ttm) REVERT: A 161 MET cc_start: 0.8615 (tpt) cc_final: 0.7962 (tpt) REVERT: B 523 LEU cc_start: 0.9332 (mt) cc_final: 0.9029 (mt) REVERT: B 632 ASP cc_start: 0.7654 (t0) cc_final: 0.7416 (t0) REVERT: B 653 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7679 (tm-30) REVERT: C 424 ILE cc_start: 0.9199 (mp) cc_final: 0.8981 (mt) REVERT: D 523 LEU cc_start: 0.9307 (mt) cc_final: 0.9049 (mt) REVERT: D 530 MET cc_start: 0.8642 (mmm) cc_final: 0.8170 (mtp) REVERT: D 540 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: D 564 HIS cc_start: 0.4954 (t-90) cc_final: 0.4595 (t-90) REVERT: D 574 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7636 (mmtp) REVERT: E 150 MET cc_start: 0.8854 (mtp) cc_final: 0.8573 (mtp) REVERT: F 523 LEU cc_start: 0.9335 (mt) cc_final: 0.9024 (mt) REVERT: F 530 MET cc_start: 0.8566 (mmm) cc_final: 0.8116 (mtp) REVERT: F 540 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: F 615 SER cc_start: 0.8488 (t) cc_final: 0.8193 (m) REVERT: F 616 ASN cc_start: 0.7975 (p0) cc_final: 0.7499 (p0) outliers start: 43 outliers final: 32 residues processed: 218 average time/residue: 0.0967 time to fit residues: 33.5911 Evaluate side-chains 208 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098038 restraints weight = 22647.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.100718 restraints weight = 15587.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102519 restraints weight = 12212.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103841 restraints weight = 10371.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.104613 restraints weight = 9270.897| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15660 Z= 0.187 Angle : 0.655 17.793 21438 Z= 0.314 Chirality : 0.046 0.256 2664 Planarity : 0.003 0.037 2565 Dihedral : 5.917 53.846 3864 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.29 % Allowed : 14.10 % Favored : 83.62 % 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: 0.32 (0.19), residues: 1731 helix: 1.10 (0.24), residues: 501 sheet: 0.48 (0.21), residues: 468 loop : -0.49 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.015 0.001 TYR A 217 PHE 0.022 0.002 PHE E 159 TRP 0.015 0.001 TRP B 631 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00446 (15540) covalent geometry : angle 0.63154 (21102) SS BOND : bond 0.00288 ( 24) SS BOND : angle 0.98968 ( 48) hydrogen bonds : bond 0.04300 ( 630) hydrogen bonds : angle 4.91671 ( 1809) link_ALPHA1-3 : bond 0.01106 ( 3) link_ALPHA1-3 : angle 1.71177 ( 9) link_ALPHA1-6 : bond 0.00203 ( 3) link_ALPHA1-6 : angle 1.57115 ( 9) link_BETA1-4 : bond 0.00402 ( 27) link_BETA1-4 : angle 1.29644 ( 81) link_NAG-ASN : bond 0.00182 ( 63) link_NAG-ASN : angle 1.70166 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.473 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7161 (ttm) REVERT: A 161 MET cc_start: 0.8688 (tpt) cc_final: 0.8126 (tpt) REVERT: B 653 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7777 (tm-30) REVERT: C 424 ILE cc_start: 0.9279 (mp) cc_final: 0.9013 (mt) REVERT: D 530 MET cc_start: 0.8646 (mmm) cc_final: 0.8153 (mtp) REVERT: D 574 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7754 (mmtp) REVERT: E 150 MET cc_start: 0.8901 (mtp) cc_final: 0.8626 (mtp) REVERT: F 530 MET cc_start: 0.8558 (mmm) cc_final: 0.8184 (mtp) REVERT: F 615 SER cc_start: 0.8431 (t) cc_final: 0.8134 (m) REVERT: F 616 ASN cc_start: 0.7996 (p0) cc_final: 0.7515 (p0) outliers start: 36 outliers final: 30 residues processed: 209 average time/residue: 0.1003 time to fit residues: 33.2365 Evaluate side-chains 204 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 163 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 137 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- 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** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.100932 restraints weight = 22502.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103693 restraints weight = 15306.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105587 restraints weight = 11919.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106757 restraints weight = 10046.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107739 restraints weight = 9010.569| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15660 Z= 0.133 Angle : 0.610 15.224 21438 Z= 0.297 Chirality : 0.045 0.255 2664 Planarity : 0.003 0.035 2565 Dihedral : 5.785 53.939 3864 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.03 % Allowed : 14.79 % Favored : 83.17 % 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: 1731 helix: 1.14 (0.25), residues: 483 sheet: 0.36 (0.21), residues: 510 loop : -0.49 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 542 TYR 0.013 0.001 TYR C 191 PHE 0.013 0.001 PHE E 159 TRP 0.082 0.002 TRP A 112 HIS 0.004 0.001 HIS F 564 Details of bonding type rmsd covalent geometry : bond 0.00306 (15540) covalent geometry : angle 0.58897 (21102) SS BOND : bond 0.00254 ( 24) SS BOND : angle 0.83195 ( 48) hydrogen bonds : bond 0.04050 ( 630) hydrogen bonds : angle 4.90330 ( 1809) link_ALPHA1-3 : bond 0.01056 ( 3) link_ALPHA1-3 : angle 1.42700 ( 9) link_ALPHA1-6 : bond 0.00191 ( 3) link_ALPHA1-6 : angle 1.61186 ( 9) link_BETA1-4 : bond 0.00438 ( 27) link_BETA1-4 : angle 1.23098 ( 81) link_NAG-ASN : bond 0.00175 ( 63) link_NAG-ASN : angle 1.54196 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.599 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: symmetry clash REVERT: A 95 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6747 (ttm) REVERT: A 161 MET cc_start: 0.8714 (tpt) cc_final: 0.8091 (tpt) REVERT: B 653 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7758 (tm-30) REVERT: C 424 ILE cc_start: 0.9243 (mp) cc_final: 0.9030 (mt) REVERT: D 523 LEU cc_start: 0.9308 (mt) cc_final: 0.9063 (mt) REVERT: D 530 MET cc_start: 0.8630 (mmm) cc_final: 0.8039 (mtp) REVERT: D 574 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7712 (mmtp) REVERT: E 150 MET cc_start: 0.8874 (mtp) cc_final: 0.8589 (mtp) REVERT: E 161 MET cc_start: 0.8575 (tpp) cc_final: 0.8283 (mmm) REVERT: F 523 LEU cc_start: 0.9319 (mt) cc_final: 0.9093 (mt) REVERT: F 530 MET cc_start: 0.8470 (mmm) cc_final: 0.8099 (mtp) REVERT: F 615 SER cc_start: 0.8373 (t) cc_final: 0.8133 (m) REVERT: F 616 ASN cc_start: 0.8004 (p0) cc_final: 0.7507 (p0) REVERT: F 653 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7469 (tm-30) outliers start: 32 outliers final: 29 residues processed: 207 average time/residue: 0.0994 time to fit residues: 32.4995 Evaluate side-chains 206 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 78 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN E 170 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN F 625 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103026 restraints weight = 22604.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105894 restraints weight = 15623.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107863 restraints weight = 12296.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109127 restraints weight = 10495.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109999 restraints weight = 9426.187| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15660 Z= 0.119 Angle : 0.596 14.920 21438 Z= 0.291 Chirality : 0.045 0.253 2664 Planarity : 0.003 0.034 2565 Dihedral : 5.653 54.414 3864 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.22 % Allowed : 14.98 % Favored : 82.79 % 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: 0.35 (0.20), residues: 1731 helix: 1.19 (0.25), residues: 483 sheet: 0.39 (0.21), residues: 510 loop : -0.44 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 542 TYR 0.011 0.001 TYR C 191 PHE 0.012 0.001 PHE E 159 TRP 0.021 0.001 TRP A 112 HIS 0.002 0.000 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00267 (15540) covalent geometry : angle 0.57665 (21102) SS BOND : bond 0.00238 ( 24) SS BOND : angle 0.75440 ( 48) hydrogen bonds : bond 0.03908 ( 630) hydrogen bonds : angle 4.78283 ( 1809) link_ALPHA1-3 : bond 0.01023 ( 3) link_ALPHA1-3 : angle 1.30689 ( 9) link_ALPHA1-6 : bond 0.00204 ( 3) link_ALPHA1-6 : angle 1.60295 ( 9) link_BETA1-4 : bond 0.00455 ( 27) link_BETA1-4 : angle 1.20864 ( 81) link_NAG-ASN : bond 0.00187 ( 63) link_NAG-ASN : angle 1.47198 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2072.36 seconds wall clock time: 36 minutes 54.54 seconds (2214.54 seconds total)