Starting phenix.real_space_refine on Wed Mar 4 20:43:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8z_23242/03_2026/7l8z_23242.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8z_23242/03_2026/7l8z_23242.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/7l8z_23242/03_2026/7l8z_23242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8z_23242/03_2026/7l8z_23242.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8z_23242/03_2026/7l8z_23242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8z_23242/03_2026/7l8z_23242.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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 9951 2.51 5 N 2696 2.21 5 O 3238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 15989 Number of models: 1 Model: "" Number of chains: 36 Chain: "H" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "L" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 425 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'TRANS': 84} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'UNK:plan-1': 85} Unresolved non-hydrogen planarities: 85 Chain: "A" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3516 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 2 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1086 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "C" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3521 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 2 Chain: "E" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1068 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "D" Number of atoms: 3443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3443 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 4 Chain: "F" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1091 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.58, per 1000 atoms: 0.22 Number of scatterers: 15989 At special positions: 0 Unit cell: (125.66, 126.69, 155.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 3238 8.00 N 2696 7.00 C 9951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.43 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS E 561 " distance=2.07 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 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=2.14 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.01 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.77 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA K 3 " - " MAN K 6 " " BMA T 3 " - " MAN T 5 " " BMA Z 3 " - " MAN Z 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 241 " " NAG A 603 " - " ASN A 276 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 133 " " NAG A 609 " - " ASN A 289 " " NAG A 610 " - " ASN A 137 " " NAG A 611 " - " ASN A 363 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 160 " " NAG C 609 " - " ASN C 133 " " NAG C 610 " - " ASN C 355 " " NAG C 611 " - " ASN C 363 " " NAG D 601 " - " ASN D 241 " " NAG D 602 " - " ASN D 276 " " NAG D 603 " - " ASN D 392 " " NAG D 604 " - " ASN D 339 " " NAG D 605 " - " ASN D 332 " " NAG D 606 " - " ASN D 295 " " NAG D 607 " - " ASN D 301 " " NAG D 608 " - " ASN D 133 " " NAG D 609 " - " ASN D 355 " " NAG D 610 " - " ASN D 289 " " NAG D 611 " - " ASN D 137 " " NAG E 701 " - " ASN E 637 " " NAG E 702 " - " ASN E 611 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 332 " " NAG J 1 " - " ASN A 295 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN C 332 " " NAG S 1 " - " ASN C 448 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN D 234 " " NAG X 1 " - " ASN D 386 " " NAG Y 1 " - " ASN D 448 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN D 156 " " NAG b 1 " - " ASN D 160 " " NAG c 1 " - " ASN D 197 " " NAG d 1 " - " ASN D 363 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 741.4 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 31 sheets defined 31.0% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'H' and resid 37 through 41 removed outlier: 3.693A pdb=" N UNK H 40 " --> pdb=" O UNK H 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.549A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 350 removed outlier: 4.746A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.707A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 5.085A 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 545 through 550 Processing helix chain 'B' and resid 563 through 567 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.847A pdb=" N HIS C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.158A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.569A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.331A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 542 through 547 Processing helix chain 'E' and resid 548 through 550 No H-bonds generated for 'chain 'E' and resid 548 through 550' Processing helix chain 'E' and resid 563 through 567 Processing helix chain 'E' and resid 568 through 596 Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 659 Processing helix chain 'E' and resid 660 through 663 Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.643A pdb=" N CYS D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.085A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 334 through 351 removed outlier: 3.566A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 476 through 484 removed outlier: 4.591A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.143A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 535 Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 544 through 546 No H-bonds generated for 'chain 'F' and resid 544 through 546' Processing helix chain 'F' and resid 564 through 567 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 removed outlier: 6.251A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 54 through 56 removed outlier: 3.790A pdb=" N UNK H 54 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N UNK H 31 " --> pdb=" O UNK H 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'L' and resid 58 through 59 removed outlier: 3.558A pdb=" N UNK L 62 " --> pdb=" O UNK L 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.403A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA9, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB1, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.344A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.724A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.834A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.528A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.865A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.613A pdb=" N THR C 132 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.773A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.772A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.008A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.830A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.008A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.583A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 494 through 499 removed outlier: 4.583A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.367A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.678A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.940A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.736A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1629 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: 2.90 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 5200 1.35 - 1.51: 6379 1.51 - 1.67: 4541 1.67 - 1.82: 118 1.82 - 1.98: 19 Bond restraints: 16257 Sorted by residual: bond pdb=" NE ARG D 503 " pdb=" CZ ARG D 503 " ideal model delta sigma weight residual 1.326 1.412 -0.086 1.10e-02 8.26e+03 6.17e+01 bond pdb=" CB LEU E 663 " pdb=" CG LEU E 663 " ideal model delta sigma weight residual 1.530 1.674 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" CB HIS F 564 " pdb=" CG HIS F 564 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.27e+01 bond pdb=" CB ASN A 67 " pdb=" CG ASN A 67 " ideal model delta sigma weight residual 1.516 1.356 0.160 2.50e-02 1.60e+03 4.09e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.02e+01 ... (remaining 16252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 20942 3.61 - 7.23: 1098 7.23 - 10.84: 52 10.84 - 14.46: 2 14.46 - 18.07: 4 Bond angle restraints: 22098 Sorted by residual: angle pdb=" N GLN C 428 " pdb=" CA GLN C 428 " pdb=" C GLN C 428 " ideal model delta sigma weight residual 114.04 95.97 18.07 1.24e+00 6.50e-01 2.12e+02 angle pdb=" N GLN D 428 " pdb=" CA GLN D 428 " pdb=" C GLN D 428 " ideal model delta sigma weight residual 114.04 97.50 16.54 1.24e+00 6.50e-01 1.78e+02 angle pdb=" N LEU F 629 " pdb=" CA LEU F 629 " pdb=" C LEU F 629 " ideal model delta sigma weight residual 110.55 94.69 15.86 1.35e+00 5.49e-01 1.38e+02 angle pdb=" N VAL D 242 " pdb=" CA VAL D 242 " pdb=" C VAL D 242 " ideal model delta sigma weight residual 109.34 127.10 -17.76 2.08e+00 2.31e-01 7.29e+01 angle pdb=" C GLU D 492 " pdb=" N PRO D 493 " pdb=" CA PRO D 493 " ideal model delta sigma weight residual 119.56 128.06 -8.50 1.02e+00 9.61e-01 6.94e+01 ... (remaining 22093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 10679 21.21 - 42.43: 207 42.43 - 63.64: 81 63.64 - 84.85: 40 84.85 - 106.07: 21 Dihedral angle restraints: 11028 sinusoidal: 5441 harmonic: 5587 Sorted by residual: dihedral pdb=" CB CYS D 228 " pdb=" SG CYS D 228 " pdb=" SG CYS D 239 " pdb=" CB CYS D 239 " ideal model delta sinusoidal sigma weight residual 93.00 176.67 -83.67 1 1.00e+01 1.00e-02 8.54e+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 93.00 158.96 -65.96 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.73 -65.73 1 1.00e+01 1.00e-02 5.65e+01 ... (remaining 11025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.278: 2550 0.278 - 0.557: 270 0.557 - 0.835: 1 0.835 - 1.114: 0 1.114 - 1.392: 2 Chirality restraints: 2823 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.63e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 2820 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 601 " 0.290 2.00e-02 2.50e+03 2.42e-01 7.29e+02 pdb=" C7 NAG D 601 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG D 601 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG D 601 " -0.406 2.00e-02 2.50e+03 pdb=" O7 NAG D 601 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " -0.155 2.00e-02 2.50e+03 1.93e-01 4.67e+02 pdb=" CG ASN D 234 " 0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " 0.332 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " -0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 137 " -0.134 2.00e-02 2.50e+03 1.89e-01 4.47e+02 pdb=" CG ASN D 137 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN D 137 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN D 137 " 0.332 2.00e-02 2.50e+03 pdb=" C1 NAG D 611 " -0.215 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 161 2.62 - 3.19: 14142 3.19 - 3.76: 22602 3.76 - 4.33: 33269 4.33 - 4.90: 51962 Nonbonded interactions: 122136 Sorted by model distance: nonbonded pdb=" O3 NAG D 601 " pdb=" O7 NAG D 601 " model vdw 2.046 3.040 nonbonded pdb=" O3 NAG W 1 " pdb=" O7 NAG W 1 " model vdw 2.052 3.040 nonbonded pdb=" N LEU F 629 " pdb=" O LEU F 629 " model vdw 2.216 2.496 nonbonded pdb=" N GLN C 428 " pdb=" N ARG C 429 " model vdw 2.327 2.560 nonbonded pdb=" N UNK L 45 " pdb=" O UNK L 49 " model vdw 2.337 3.120 ... (remaining 122131 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 56 or resid 63 through 140 or resid 151 through \ 611)) selection = (chain 'C' and (resid 33 through 56 or resid 63 through 140 or resid 151 through \ 611)) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 521 through 550 or resid 561 through 701)) selection = (chain 'E' and (resid 521 through 550 or resid 561 through 701)) selection = (chain 'F' and (resid 521 through 550 or resid 561 through 701)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'K' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.390 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.025 0.743 16386 Z= 1.317 Angle : 1.827 22.448 22451 Z= 1.126 Chirality : 0.153 1.392 2823 Planarity : 0.010 0.242 2699 Dihedral : 11.795 106.065 7292 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.06 % 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: 0.76 (0.20), residues: 1700 helix: -0.10 (0.24), residues: 420 sheet: 0.85 (0.22), residues: 464 loop : 0.86 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 429 TYR 0.051 0.008 TYR D 40 PHE 0.030 0.006 PHE D 383 TRP 0.074 0.009 TRP E 610 HIS 0.015 0.003 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.02335 (16257) covalent geometry : angle 1.75417 (22098) SS BOND : bond 0.14622 ( 34) SS BOND : angle 4.08742 ( 68) hydrogen bonds : bond 0.18330 ( 607) hydrogen bonds : angle 7.47904 ( 1629) link_ALPHA1-2 : bond 0.08015 ( 2) link_ALPHA1-2 : angle 4.31461 ( 6) link_ALPHA1-3 : bond 0.08409 ( 3) link_ALPHA1-3 : angle 4.04938 ( 9) link_ALPHA1-6 : bond 0.05647 ( 3) link_ALPHA1-6 : angle 4.16944 ( 9) link_BETA1-4 : bond 0.06917 ( 26) link_BETA1-4 : angle 4.66144 ( 78) link_NAG-ASN : bond 0.07790 ( 61) link_NAG-ASN : angle 4.48897 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8667 (mttm) cc_final: 0.7927 (mtpt) REVERT: A 80 ASN cc_start: 0.8414 (m-40) cc_final: 0.8062 (m-40) REVERT: A 115 SER cc_start: 0.9169 (m) cc_final: 0.8766 (t) REVERT: A 163 THR cc_start: 0.9297 (p) cc_final: 0.9041 (t) REVERT: B 607 ASN cc_start: 0.8279 (m-40) cc_final: 0.8007 (m-40) REVERT: B 613 THR cc_start: 0.9177 (p) cc_final: 0.8732 (t) REVERT: B 639 THR cc_start: 0.8895 (m) cc_final: 0.8541 (p) REVERT: C 80 ASN cc_start: 0.8489 (m-40) cc_final: 0.8278 (m-40) REVERT: C 217 TYR cc_start: 0.9206 (m-80) cc_final: 0.9000 (m-80) REVERT: C 264 SER cc_start: 0.8465 (m) cc_final: 0.8254 (m) REVERT: C 426 MET cc_start: 0.8227 (tpp) cc_final: 0.7985 (tpp) REVERT: C 427 TRP cc_start: 0.8339 (t-100) cc_final: 0.7908 (t-100) REVERT: E 585 ARG cc_start: 0.8801 (mtt-85) cc_final: 0.8278 (mtm180) REVERT: D 128 THR cc_start: 0.9236 (m) cc_final: 0.8996 (p) REVERT: F 545 LEU cc_start: 0.8840 (tp) cc_final: 0.8610 (tp) REVERT: F 637 ASN cc_start: 0.7671 (p0) cc_final: 0.6929 (t0) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.1361 time to fit residues: 82.4652 Evaluate side-chains 208 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 616 ASN B 653 GLN C 72 HIS E 564 HIS E 577 GLN D 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.125100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104013 restraints weight = 28151.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106942 restraints weight = 16512.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108903 restraints weight = 11732.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110207 restraints weight = 9349.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111068 restraints weight = 7992.739| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16386 Z= 0.196 Angle : 0.843 18.288 22451 Z= 0.411 Chirality : 0.049 0.330 2823 Planarity : 0.004 0.041 2699 Dihedral : 9.007 83.865 3999 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.46 % Allowed : 9.33 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.88 (0.20), residues: 1700 helix: 1.07 (0.26), residues: 426 sheet: 0.59 (0.23), residues: 454 loop : 0.48 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.018 0.002 TYR F 643 PHE 0.019 0.003 PHE A 383 TRP 0.032 0.002 TRP C 427 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00426 (16257) covalent geometry : angle 0.75573 (22098) SS BOND : bond 0.00348 ( 34) SS BOND : angle 1.32449 ( 68) hydrogen bonds : bond 0.06117 ( 607) hydrogen bonds : angle 5.69978 ( 1629) link_ALPHA1-2 : bond 0.01161 ( 2) link_ALPHA1-2 : angle 1.87692 ( 6) link_ALPHA1-3 : bond 0.01778 ( 3) link_ALPHA1-3 : angle 2.05807 ( 9) link_ALPHA1-6 : bond 0.00920 ( 3) link_ALPHA1-6 : angle 1.45809 ( 9) link_BETA1-4 : bond 0.00747 ( 26) link_BETA1-4 : angle 2.78468 ( 78) link_NAG-ASN : bond 0.00556 ( 61) link_NAG-ASN : angle 3.70548 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 SER cc_start: 0.8927 (m) cc_final: 0.8581 (t) REVERT: A 199 SER cc_start: 0.9131 (p) cc_final: 0.8822 (t) REVERT: A 231 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7863 (ptmt) REVERT: B 543 ASN cc_start: 0.8375 (t0) cc_final: 0.8078 (t0) REVERT: B 586 TYR cc_start: 0.9165 (t80) cc_final: 0.8926 (t80) REVERT: B 613 THR cc_start: 0.9125 (p) cc_final: 0.8784 (t) REVERT: B 639 THR cc_start: 0.8916 (m) cc_final: 0.8711 (p) REVERT: B 654 GLU cc_start: 0.7877 (tp30) cc_final: 0.7621 (tp30) REVERT: C 51 THR cc_start: 0.9320 (m) cc_final: 0.9084 (p) REVERT: C 103 GLN cc_start: 0.8140 (tp40) cc_final: 0.7571 (tp-100) REVERT: C 215 ILE cc_start: 0.9203 (mm) cc_final: 0.8878 (tt) REVERT: C 426 MET cc_start: 0.8102 (tpp) cc_final: 0.7767 (tpp) REVERT: E 542 ARG cc_start: 0.7648 (ttm110) cc_final: 0.7363 (ttm110) REVERT: D 125 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9102 (tp) REVERT: F 637 ASN cc_start: 0.7421 (p0) cc_final: 0.6940 (t0) outliers start: 38 outliers final: 24 residues processed: 276 average time/residue: 0.1147 time to fit residues: 48.1509 Evaluate side-chains 226 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 646 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 55 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 23 optimal weight: 0.0870 chunk 185 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN E 564 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101192 restraints weight = 28931.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104151 restraints weight = 16758.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106165 restraints weight = 11872.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107321 restraints weight = 9406.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108287 restraints weight = 8125.925| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.181 Angle : 0.728 15.022 22451 Z= 0.356 Chirality : 0.047 0.357 2823 Planarity : 0.004 0.039 2699 Dihedral : 7.852 76.228 3999 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.56 % Allowed : 10.24 % Favored : 86.20 % 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: 0.88 (0.21), residues: 1700 helix: 1.41 (0.27), residues: 415 sheet: 0.52 (0.22), residues: 489 loop : 0.33 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 298 TYR 0.019 0.002 TYR C 61 PHE 0.021 0.002 PHE E 522 TRP 0.021 0.002 TRP F 623 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00412 (16257) covalent geometry : angle 0.66713 (22098) SS BOND : bond 0.00641 ( 34) SS BOND : angle 1.06957 ( 68) hydrogen bonds : bond 0.05247 ( 607) hydrogen bonds : angle 5.31877 ( 1629) link_ALPHA1-2 : bond 0.00915 ( 2) link_ALPHA1-2 : angle 1.81678 ( 6) link_ALPHA1-3 : bond 0.01356 ( 3) link_ALPHA1-3 : angle 1.67642 ( 9) link_ALPHA1-6 : bond 0.00920 ( 3) link_ALPHA1-6 : angle 1.75872 ( 9) link_BETA1-4 : bond 0.00658 ( 26) link_BETA1-4 : angle 2.08486 ( 78) link_NAG-ASN : bond 0.00479 ( 61) link_NAG-ASN : angle 2.92624 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9203 (p) cc_final: 0.8891 (t) REVERT: A 211 GLU cc_start: 0.8487 (tp30) cc_final: 0.8221 (tp30) REVERT: A 231 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7921 (ptmt) REVERT: B 543 ASN cc_start: 0.8488 (t0) cc_final: 0.8246 (t0) REVERT: B 586 TYR cc_start: 0.9217 (t80) cc_final: 0.8988 (t80) REVERT: B 613 THR cc_start: 0.9257 (p) cc_final: 0.9021 (t) REVERT: B 647 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7497 (mt-10) REVERT: B 648 GLU cc_start: 0.8097 (pt0) cc_final: 0.7873 (pt0) REVERT: B 654 GLU cc_start: 0.8052 (tp30) cc_final: 0.7786 (tp30) REVERT: C 51 THR cc_start: 0.9372 (m) cc_final: 0.9067 (p) REVERT: C 103 GLN cc_start: 0.8117 (tp40) cc_final: 0.7709 (tm-30) REVERT: C 217 TYR cc_start: 0.9013 (m-80) cc_final: 0.8481 (m-80) REVERT: C 258 GLN cc_start: 0.8958 (mt0) cc_final: 0.8748 (mt0) REVERT: E 632 ASP cc_start: 0.8173 (m-30) cc_final: 0.7963 (m-30) REVERT: D 125 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9117 (tp) REVERT: F 637 ASN cc_start: 0.7550 (p0) cc_final: 0.6896 (t0) outliers start: 55 outliers final: 38 residues processed: 257 average time/residue: 0.1187 time to fit residues: 46.0316 Evaluate side-chains 236 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 13 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN E 564 HIS E 577 GLN D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102420 restraints weight = 28452.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105437 restraints weight = 16372.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107438 restraints weight = 11527.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108630 restraints weight = 9149.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109617 restraints weight = 7848.638| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16386 Z= 0.133 Angle : 0.679 22.066 22451 Z= 0.325 Chirality : 0.045 0.357 2823 Planarity : 0.003 0.036 2699 Dihedral : 6.943 68.450 3999 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.37 % Allowed : 11.34 % Favored : 85.29 % 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: 0.82 (0.21), residues: 1700 helix: 1.51 (0.27), residues: 423 sheet: 0.52 (0.22), residues: 483 loop : 0.14 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 542 TYR 0.014 0.001 TYR F 643 PHE 0.014 0.002 PHE E 522 TRP 0.014 0.001 TRP D 427 HIS 0.015 0.001 HIS E 564 Details of bonding type rmsd covalent geometry : bond 0.00295 (16257) covalent geometry : angle 0.60315 (22098) SS BOND : bond 0.00338 ( 34) SS BOND : angle 0.95650 ( 68) hydrogen bonds : bond 0.04436 ( 607) hydrogen bonds : angle 5.01624 ( 1629) link_ALPHA1-2 : bond 0.00858 ( 2) link_ALPHA1-2 : angle 1.87555 ( 6) link_ALPHA1-3 : bond 0.01273 ( 3) link_ALPHA1-3 : angle 1.73704 ( 9) link_ALPHA1-6 : bond 0.00871 ( 3) link_ALPHA1-6 : angle 1.81575 ( 9) link_BETA1-4 : bond 0.00555 ( 26) link_BETA1-4 : angle 1.74760 ( 78) link_NAG-ASN : bond 0.00387 ( 61) link_NAG-ASN : angle 3.24731 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9253 (p) cc_final: 0.8957 (t) REVERT: A 231 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7966 (ptmt) REVERT: B 586 TYR cc_start: 0.9214 (t80) cc_final: 0.8930 (t80) REVERT: B 621 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 654 GLU cc_start: 0.8022 (tp30) cc_final: 0.7701 (tp30) REVERT: C 51 THR cc_start: 0.9388 (m) cc_final: 0.9049 (p) REVERT: C 217 TYR cc_start: 0.8883 (m-80) cc_final: 0.8599 (m-80) REVERT: C 258 GLN cc_start: 0.8997 (mt0) cc_final: 0.8779 (mt0) REVERT: D 297 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8420 (p) outliers start: 52 outliers final: 32 residues processed: 257 average time/residue: 0.1218 time to fit residues: 46.8542 Evaluate side-chains 235 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 51 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 80 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099813 restraints weight = 28795.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102705 restraints weight = 16734.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104628 restraints weight = 11892.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105918 restraints weight = 9496.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106569 restraints weight = 8152.560| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.183 Angle : 0.706 20.416 22451 Z= 0.337 Chirality : 0.047 0.357 2823 Planarity : 0.004 0.039 2699 Dihedral : 6.614 62.775 3999 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.47 % Rotamer: Outliers : 3.69 % Allowed : 11.80 % Favored : 84.51 % 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: 0.71 (0.21), residues: 1700 helix: 1.56 (0.27), residues: 423 sheet: 0.52 (0.23), residues: 449 loop : -0.04 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 542 TYR 0.015 0.002 TYR D 40 PHE 0.013 0.002 PHE A 383 TRP 0.014 0.001 TRP D 427 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00426 (16257) covalent geometry : angle 0.63764 (22098) SS BOND : bond 0.00374 ( 34) SS BOND : angle 1.11714 ( 68) hydrogen bonds : bond 0.04511 ( 607) hydrogen bonds : angle 5.00370 ( 1629) link_ALPHA1-2 : bond 0.00844 ( 2) link_ALPHA1-2 : angle 1.72584 ( 6) link_ALPHA1-3 : bond 0.01293 ( 3) link_ALPHA1-3 : angle 2.01882 ( 9) link_ALPHA1-6 : bond 0.00844 ( 3) link_ALPHA1-6 : angle 1.76541 ( 9) link_BETA1-4 : bond 0.00534 ( 26) link_BETA1-4 : angle 1.74214 ( 78) link_NAG-ASN : bond 0.00422 ( 61) link_NAG-ASN : angle 3.14455 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 202 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9324 (p) cc_final: 0.8998 (t) REVERT: A 231 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7966 (ptmt) REVERT: B 551 GLN cc_start: 0.6208 (OUTLIER) cc_final: 0.5110 (pm20) REVERT: B 586 TYR cc_start: 0.9254 (t80) cc_final: 0.8909 (t80) REVERT: B 654 GLU cc_start: 0.7995 (tp30) cc_final: 0.7639 (tp30) REVERT: C 51 THR cc_start: 0.9375 (m) cc_final: 0.9168 (p) REVERT: C 103 GLN cc_start: 0.8007 (tp40) cc_final: 0.7733 (tm-30) REVERT: C 217 TYR cc_start: 0.8963 (m-80) cc_final: 0.8458 (m-80) REVERT: C 258 GLN cc_start: 0.9032 (mt0) cc_final: 0.8680 (mt0) REVERT: D 297 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8463 (p) outliers start: 57 outliers final: 36 residues processed: 242 average time/residue: 0.1124 time to fit residues: 41.3527 Evaluate side-chains 230 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS E 563 GLN E 577 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099107 restraints weight = 28842.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101860 restraints weight = 17284.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103687 restraints weight = 12476.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104906 restraints weight = 10088.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105622 restraints weight = 8718.802| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 16386 Z= 0.185 Angle : 0.713 18.153 22451 Z= 0.339 Chirality : 0.048 0.703 2823 Planarity : 0.004 0.038 2699 Dihedral : 6.600 55.475 3999 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 4.54 % Allowed : 11.34 % Favored : 84.12 % 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: 0.55 (0.21), residues: 1700 helix: 1.52 (0.27), residues: 426 sheet: 0.41 (0.23), residues: 449 loop : -0.19 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 542 TYR 0.014 0.002 TYR D 217 PHE 0.013 0.002 PHE A 383 TRP 0.016 0.001 TRP A 427 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00431 (16257) covalent geometry : angle 0.63895 (22098) SS BOND : bond 0.00461 ( 34) SS BOND : angle 0.99082 ( 68) hydrogen bonds : bond 0.04513 ( 607) hydrogen bonds : angle 4.98336 ( 1629) link_ALPHA1-2 : bond 0.00825 ( 2) link_ALPHA1-2 : angle 1.79046 ( 6) link_ALPHA1-3 : bond 0.01397 ( 3) link_ALPHA1-3 : angle 1.99131 ( 9) link_ALPHA1-6 : bond 0.00808 ( 3) link_ALPHA1-6 : angle 1.67969 ( 9) link_BETA1-4 : bond 0.00478 ( 26) link_BETA1-4 : angle 1.60146 ( 78) link_NAG-ASN : bond 0.00651 ( 61) link_NAG-ASN : angle 3.33276 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 200 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.4917 (pm20) REVERT: A 199 SER cc_start: 0.9391 (p) cc_final: 0.9027 (t) REVERT: A 231 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7969 (ptmt) REVERT: B 551 GLN cc_start: 0.6077 (OUTLIER) cc_final: 0.4989 (pm20) REVERT: B 586 TYR cc_start: 0.9258 (t80) cc_final: 0.8924 (t80) REVERT: B 621 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8318 (tm-30) REVERT: B 654 GLU cc_start: 0.7953 (tp30) cc_final: 0.7662 (tp30) REVERT: C 217 TYR cc_start: 0.8951 (m-80) cc_final: 0.8495 (m-80) REVERT: C 258 GLN cc_start: 0.9001 (mt0) cc_final: 0.8682 (mt0) REVERT: C 340 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: E 605 CYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8407 (m) REVERT: D 40 TYR cc_start: 0.9317 (t80) cc_final: 0.9089 (t80) REVERT: D 125 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9082 (tt) REVERT: D 243 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.8117 (t) REVERT: D 282 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8847 (mttm) REVERT: D 297 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8596 (p) outliers start: 70 outliers final: 47 residues processed: 249 average time/residue: 0.1195 time to fit residues: 45.1570 Evaluate side-chains 242 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 51 optimal weight: 0.0270 chunk 95 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099954 restraints weight = 28642.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102678 restraints weight = 17279.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104489 restraints weight = 12527.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105541 restraints weight = 10121.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106467 restraints weight = 8843.341| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16386 Z= 0.152 Angle : 0.681 16.381 22451 Z= 0.325 Chirality : 0.047 0.632 2823 Planarity : 0.003 0.037 2699 Dihedral : 6.343 48.303 3999 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.59 % Favored : 96.29 % Rotamer: Outliers : 4.21 % Allowed : 11.47 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1700 helix: 1.66 (0.27), residues: 423 sheet: 0.40 (0.24), residues: 444 loop : -0.15 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 617 TYR 0.011 0.001 TYR C 40 PHE 0.017 0.002 PHE F 522 TRP 0.012 0.001 TRP F 631 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00349 (16257) covalent geometry : angle 0.61097 (22098) SS BOND : bond 0.00518 ( 34) SS BOND : angle 1.08663 ( 68) hydrogen bonds : bond 0.04263 ( 607) hydrogen bonds : angle 4.93399 ( 1629) link_ALPHA1-2 : bond 0.00801 ( 2) link_ALPHA1-2 : angle 1.85983 ( 6) link_ALPHA1-3 : bond 0.01219 ( 3) link_ALPHA1-3 : angle 1.84285 ( 9) link_ALPHA1-6 : bond 0.00864 ( 3) link_ALPHA1-6 : angle 1.64572 ( 9) link_BETA1-4 : bond 0.00489 ( 26) link_BETA1-4 : angle 1.51407 ( 78) link_NAG-ASN : bond 0.00515 ( 61) link_NAG-ASN : angle 3.16467 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.4700 (pm20) REVERT: A 199 SER cc_start: 0.9389 (p) cc_final: 0.9033 (t) REVERT: A 231 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8023 (ptmt) REVERT: B 551 GLN cc_start: 0.6084 (OUTLIER) cc_final: 0.5160 (pm20) REVERT: B 586 TYR cc_start: 0.9257 (t80) cc_final: 0.8905 (t80) REVERT: B 654 GLU cc_start: 0.7884 (tp30) cc_final: 0.7609 (tp30) REVERT: C 217 TYR cc_start: 0.9002 (m-80) cc_final: 0.8666 (m-80) REVERT: C 258 GLN cc_start: 0.8998 (mt0) cc_final: 0.8700 (mt0) REVERT: C 340 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: D 297 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8626 (p) outliers start: 65 outliers final: 48 residues processed: 247 average time/residue: 0.1230 time to fit residues: 45.4819 Evaluate side-chains 242 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099028 restraints weight = 29002.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101803 restraints weight = 17444.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103621 restraints weight = 12617.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104813 restraints weight = 10203.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105539 restraints weight = 8851.219| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16386 Z= 0.166 Angle : 0.685 15.067 22451 Z= 0.326 Chirality : 0.046 0.563 2823 Planarity : 0.003 0.037 2699 Dihedral : 6.241 54.554 3999 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.88 % Favored : 96.00 % Rotamer: Outliers : 4.34 % Allowed : 11.73 % Favored : 83.93 % 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: 0.58 (0.21), residues: 1700 helix: 1.67 (0.27), residues: 423 sheet: 0.38 (0.23), residues: 442 loop : -0.21 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 617 TYR 0.012 0.001 TYR C 40 PHE 0.016 0.002 PHE F 522 TRP 0.012 0.001 TRP C 479 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00388 (16257) covalent geometry : angle 0.62181 (22098) SS BOND : bond 0.00349 ( 34) SS BOND : angle 0.88864 ( 68) hydrogen bonds : bond 0.04294 ( 607) hydrogen bonds : angle 4.91660 ( 1629) link_ALPHA1-2 : bond 0.00793 ( 2) link_ALPHA1-2 : angle 1.81145 ( 6) link_ALPHA1-3 : bond 0.01215 ( 3) link_ALPHA1-3 : angle 1.87086 ( 9) link_ALPHA1-6 : bond 0.00784 ( 3) link_ALPHA1-6 : angle 1.51693 ( 9) link_BETA1-4 : bond 0.00485 ( 26) link_BETA1-4 : angle 1.53285 ( 78) link_NAG-ASN : bond 0.00516 ( 61) link_NAG-ASN : angle 3.04268 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 199 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.4613 (pm20) REVERT: A 199 SER cc_start: 0.9426 (p) cc_final: 0.9066 (t) REVERT: A 231 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8002 (ptmt) REVERT: B 551 GLN cc_start: 0.6135 (OUTLIER) cc_final: 0.5191 (pm20) REVERT: B 586 TYR cc_start: 0.9267 (t80) cc_final: 0.8912 (t80) REVERT: B 654 GLU cc_start: 0.7898 (tp30) cc_final: 0.7615 (tp30) REVERT: C 217 TYR cc_start: 0.8964 (m-80) cc_final: 0.8620 (m-80) REVERT: C 258 GLN cc_start: 0.9024 (mt0) cc_final: 0.8675 (mt0) REVERT: C 340 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: D 297 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8647 (p) REVERT: F 626 MET cc_start: 0.6479 (ttm) cc_final: 0.5924 (ttm) outliers start: 67 outliers final: 54 residues processed: 243 average time/residue: 0.1254 time to fit residues: 45.9981 Evaluate side-chains 248 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 126 optimal weight: 0.4980 chunk 141 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 62 optimal weight: 0.0040 chunk 35 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 169 optimal weight: 0.0980 chunk 116 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN ** D 374 HIS ** 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 = 0.3531 r_free = 0.3531 target = 0.122636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101741 restraints weight = 28525.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104546 restraints weight = 16941.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106421 restraints weight = 12203.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107651 restraints weight = 9807.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.108448 restraints weight = 8451.839| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 16386 Z= 0.111 Angle : 0.642 14.334 22451 Z= 0.307 Chirality : 0.045 0.525 2823 Planarity : 0.003 0.038 2699 Dihedral : 5.852 53.125 3999 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.47 % Favored : 96.41 % Rotamer: Outliers : 2.85 % Allowed : 13.55 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.69 (0.21), residues: 1700 helix: 1.75 (0.27), residues: 429 sheet: 0.50 (0.23), residues: 449 loop : -0.20 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 350 TYR 0.011 0.001 TYR C 40 PHE 0.018 0.001 PHE F 522 TRP 0.015 0.001 TRP F 631 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00240 (16257) covalent geometry : angle 0.58092 (22098) SS BOND : bond 0.00246 ( 34) SS BOND : angle 0.99264 ( 68) hydrogen bonds : bond 0.03835 ( 607) hydrogen bonds : angle 4.79026 ( 1629) link_ALPHA1-2 : bond 0.00798 ( 2) link_ALPHA1-2 : angle 1.98783 ( 6) link_ALPHA1-3 : bond 0.01187 ( 3) link_ALPHA1-3 : angle 1.59708 ( 9) link_ALPHA1-6 : bond 0.00743 ( 3) link_ALPHA1-6 : angle 1.47509 ( 9) link_BETA1-4 : bond 0.00509 ( 26) link_BETA1-4 : angle 1.40193 ( 78) link_NAG-ASN : bond 0.00485 ( 61) link_NAG-ASN : angle 2.86852 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.4533 (pm20) REVERT: A 199 SER cc_start: 0.9411 (p) cc_final: 0.9018 (t) REVERT: A 231 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8020 (ptmt) REVERT: B 551 GLN cc_start: 0.6121 (OUTLIER) cc_final: 0.5236 (pm20) REVERT: B 586 TYR cc_start: 0.9229 (t80) cc_final: 0.8888 (t80) REVERT: B 654 GLU cc_start: 0.7919 (tp30) cc_final: 0.7606 (tp30) REVERT: C 217 TYR cc_start: 0.8824 (m-80) cc_final: 0.8496 (m-80) REVERT: C 258 GLN cc_start: 0.8912 (mt0) cc_final: 0.8682 (mt0) REVERT: C 498 PRO cc_start: 0.8769 (Cg_exo) cc_final: 0.8429 (Cg_endo) REVERT: D 282 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8930 (mttm) REVERT: F 588 ARG cc_start: 0.7446 (ttm170) cc_final: 0.6960 (ttm-80) outliers start: 44 outliers final: 35 residues processed: 241 average time/residue: 0.1174 time to fit residues: 42.9706 Evaluate side-chains 234 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 75 optimal weight: 2.9990 chunk 140 optimal weight: 0.2980 chunk 173 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100067 restraints weight = 28836.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.102943 restraints weight = 17002.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104828 restraints weight = 12146.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106072 restraints weight = 9735.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106801 restraints weight = 8391.152| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16386 Z= 0.147 Angle : 0.670 14.125 22451 Z= 0.321 Chirality : 0.046 0.489 2823 Planarity : 0.003 0.036 2699 Dihedral : 5.754 43.110 3999 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.12 % Rotamer: Outliers : 2.92 % Allowed : 14.26 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.58 (0.21), residues: 1700 helix: 1.65 (0.27), residues: 429 sheet: 0.34 (0.23), residues: 447 loop : -0.18 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 350 TYR 0.013 0.001 TYR C 40 PHE 0.017 0.002 PHE F 522 TRP 0.012 0.001 TRP B 631 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00345 (16257) covalent geometry : angle 0.61251 (22098) SS BOND : bond 0.00343 ( 34) SS BOND : angle 0.93382 ( 68) hydrogen bonds : bond 0.04038 ( 607) hydrogen bonds : angle 4.80497 ( 1629) link_ALPHA1-2 : bond 0.00791 ( 2) link_ALPHA1-2 : angle 1.80026 ( 6) link_ALPHA1-3 : bond 0.01137 ( 3) link_ALPHA1-3 : angle 1.54993 ( 9) link_ALPHA1-6 : bond 0.00647 ( 3) link_ALPHA1-6 : angle 1.55885 ( 9) link_BETA1-4 : bond 0.00492 ( 26) link_BETA1-4 : angle 1.48038 ( 78) link_NAG-ASN : bond 0.00471 ( 61) link_NAG-ASN : angle 2.85244 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.4502 (pm20) REVERT: A 231 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8012 (ptmt) REVERT: B 551 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5223 (pm20) REVERT: B 586 TYR cc_start: 0.9263 (t80) cc_final: 0.8916 (t80) REVERT: B 654 GLU cc_start: 0.7975 (tp30) cc_final: 0.7675 (tp30) REVERT: C 217 TYR cc_start: 0.8864 (m-80) cc_final: 0.8496 (m-80) REVERT: C 258 GLN cc_start: 0.8962 (mt0) cc_final: 0.8711 (mt0) REVERT: D 282 LYS cc_start: 0.9186 (mmtt) cc_final: 0.8959 (mttm) outliers start: 45 outliers final: 38 residues processed: 227 average time/residue: 0.1200 time to fit residues: 40.9964 Evaluate side-chains 226 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 562 GLN Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 156 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099473 restraints weight = 28793.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102330 restraints weight = 16939.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104198 restraints weight = 12126.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105421 restraints weight = 9740.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106269 restraints weight = 8399.868| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16386 Z= 0.154 Angle : 0.664 13.622 22451 Z= 0.319 Chirality : 0.046 0.487 2823 Planarity : 0.003 0.036 2699 Dihedral : 5.855 43.377 3999 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 2.98 % Allowed : 14.32 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.54 (0.21), residues: 1700 helix: 1.62 (0.27), residues: 430 sheet: 0.36 (0.23), residues: 434 loop : -0.25 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 617 TYR 0.012 0.001 TYR C 40 PHE 0.018 0.002 PHE F 522 TRP 0.024 0.001 TRP A 427 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00360 (16257) covalent geometry : angle 0.60838 (22098) SS BOND : bond 0.00334 ( 34) SS BOND : angle 0.91884 ( 68) hydrogen bonds : bond 0.04078 ( 607) hydrogen bonds : angle 4.81653 ( 1629) link_ALPHA1-2 : bond 0.00767 ( 2) link_ALPHA1-2 : angle 1.79669 ( 6) link_ALPHA1-3 : bond 0.01060 ( 3) link_ALPHA1-3 : angle 1.44419 ( 9) link_ALPHA1-6 : bond 0.00638 ( 3) link_ALPHA1-6 : angle 1.47773 ( 9) link_BETA1-4 : bond 0.00476 ( 26) link_BETA1-4 : angle 1.44659 ( 78) link_NAG-ASN : bond 0.00452 ( 61) link_NAG-ASN : angle 2.80307 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2296.51 seconds wall clock time: 40 minutes 33.36 seconds (2433.36 seconds total)