Starting phenix.real_space_refine on Sat Sep 12 12:26:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l88_23225/09_2026/7l88_23225.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l88_23225/09_2026/7l88_23225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l88_23225/09_2026/7l88_23225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l88_23225/09_2026/7l88_23225.map" model { file = "/net/cci-nas-00/data/ceres_data/7l88_23225/09_2026/7l88_23225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l88_23225/09_2026/7l88_23225.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l88_23225/09_2026/7l88_23225.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l88_23225/09_2026/7l88_23225.cif" } resolution = 3.6 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 99 5.16 5 C 9734 2.51 5 N 2622 2.21 5 O 3179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15634 Number of models: 1 Model: "" Number of chains: 43 Chain: "D" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3430 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 570 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 114} Link IDs: {'TRANS': 113} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 114 Planarities with less than four sites: {'UNK:plan-1': 114} Unresolved non-hydrogen planarities: 114 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 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 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 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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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 chiralities: 5 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 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 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 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 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 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 chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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 chiralities: 3 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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 chiralities: 2 Time building chain proxies: 3.39, per 1000 atoms: 0.22 Number of scatterers: 15634 At special positions: 0 Unit cell: (131.84, 122.57, 145.23, 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 99 16.00 O 3179 8.00 N 2622 7.00 C 9734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.08 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.06 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA X 3 " - " MAN X 4 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA g 3 " - " MAN g 5 " 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 M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 295 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 448 " " NAG A 607 " - " ASN A 355 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 448 " " NAG C 607 " - " ASN C 88 " " NAG C 608 " - " ASN C 137 " " NAG D 601 " - " ASN D 160 " " NAG D 602 " - " ASN D 301 " " NAG D 603 " - " ASN D 339 " " NAG D 604 " - " ASN D 448 " " NAG D 605 " - " ASN D 355 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN D 133 " " NAG I 1 " - " ASN D 156 " " NAG J 1 " - " ASN D 197 " " NAG K 1 " - " ASN D 234 " " NAG M 1 " - " ASN D 262 " " NAG N 1 " - " ASN D 276 " " NAG O 1 " - " ASN D 295 " " NAG P 1 " - " ASN D 332 " " NAG Q 1 " - " ASN D 386 " " NAG R 1 " - " ASN D 392 " " NAG S 1 " - " ASN D 88 " " NAG T 1 " - " ASN A 133 " " NAG U 1 " - " ASN A 156 " " NAG V 1 " - " ASN A 197 " " NAG W 1 " - " ASN A 234 " " NAG X 1 " - " ASN A 262 " " NAG Y 1 " - " ASN A 276 " " NAG Z 1 " - " ASN A 332 " " NAG a 1 " - " ASN A 386 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN A 88 " " NAG d 1 " - " ASN C 156 " " NAG e 1 " - " ASN C 197 " " NAG f 1 " - " ASN C 234 " " NAG g 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 276 " " NAG i 1 " - " ASN C 295 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 386 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 477.7 milliseconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3586 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 38 sheets defined 27.1% alpha, 65.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.750A pdb=" N ASN D 98 " --> pdb=" O MET D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 115 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 354 removed outlier: 4.070A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.517A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.509A pdb=" N LYS F 574 " --> pdb=" O HIS F 570 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.137A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.666A 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 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.909A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 570 through 597 Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.734A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.089A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.053A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 618 through 624 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 664 Processing sheet with id=AA1, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.531A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.838A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'D' and resid 169 through 176 Processing sheet with id=AA6, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.080A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 256 through 257 removed outlier: 3.586A pdb=" N SER D 375 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.684A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.735A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.884A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 393 through 396 removed outlier: 6.441A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 271 through 273 removed outlier: 7.315A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 375 " --> pdb=" O THR D 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.884A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.684A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.735A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.125A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.486A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.844A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AB7, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AB8, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.042A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.706A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.812A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.745A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.706A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.812A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.896A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.130A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.412A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.731A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AD1, first strand: chain 'C' and resid 169 through 176 Processing sheet with id=AD2, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.608A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.797A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.552A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.609A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.797A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.552A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.862A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AE1, first strand: chain 'L' and resid 21 through 23 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.775A pdb=" N UNK L 11 " --> pdb=" O UNK L 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 703 hydrogen bonds defined for protein. 1893 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: 2.39 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2602 1.31 - 1.45: 4695 1.45 - 1.59: 8403 1.59 - 1.73: 72 1.73 - 1.87: 130 Bond restraints: 15902 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.84e+01 bond pdb=" NE ARG D 503 " pdb=" CZ ARG D 503 " ideal model delta sigma weight residual 1.326 1.390 -0.064 1.10e-02 8.26e+03 3.40e+01 bond pdb=" C GLU E 621 " pdb=" O GLU E 621 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.28e-02 6.10e+03 3.04e+01 bond pdb=" CA ASN E 618 " pdb=" C ASN E 618 " ideal model delta sigma weight residual 1.526 1.453 0.074 1.37e-02 5.33e+03 2.89e+01 bond pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 1.354 1.297 0.057 1.10e-02 8.26e+03 2.70e+01 ... (remaining 15897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 20307 3.35 - 6.70: 1254 6.70 - 10.06: 62 10.06 - 13.41: 9 13.41 - 16.76: 1 Bond angle restraints: 21633 Sorted by residual: angle pdb=" N HIS F 585 " pdb=" CA HIS F 585 " pdb=" C HIS F 585 " ideal model delta sigma weight residual 110.35 97.38 12.97 1.38e+00 5.25e-01 8.83e+01 angle pdb=" N SER B 599 " pdb=" CA SER B 599 " pdb=" C SER B 599 " ideal model delta sigma weight residual 112.68 124.03 -11.35 1.33e+00 5.65e-01 7.29e+01 angle pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 119.56 127.70 -8.14 1.02e+00 9.61e-01 6.37e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 127.55 -7.99 1.02e+00 9.61e-01 6.13e+01 angle pdb=" C CYS D 239 " pdb=" N PRO D 240 " pdb=" CA PRO D 240 " ideal model delta sigma weight residual 119.56 127.47 -7.91 1.02e+00 9.61e-01 6.01e+01 ... (remaining 21628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 8484 16.53 - 33.05: 250 33.05 - 49.58: 57 49.58 - 66.11: 31 66.11 - 82.63: 17 Dihedral angle restraints: 8839 sinusoidal: 3333 harmonic: 5506 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.93 -61.93 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" C ASN E 618 " pdb=" N ASN E 618 " pdb=" CA ASN E 618 " pdb=" CB ASN E 618 " ideal model delta harmonic sigma weight residual -122.60 -104.93 -17.67 0 2.50e+00 1.60e-01 5.00e+01 dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.13 -60.13 1 1.00e+01 1.00e-02 4.82e+01 ... (remaining 8836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1964 0.121 - 0.242: 446 0.242 - 0.364: 232 0.364 - 0.485: 117 0.485 - 0.606: 5 Chirality restraints: 2764 Sorted by residual: 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 -2.67 0.27 2.00e-02 2.50e+03 1.84e+02 chirality pdb=" C1 NAG k 2 " pdb=" O4 NAG k 1 " pdb=" C2 NAG k 2 " pdb=" O5 NAG k 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.76e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.38e+02 ... (remaining 2761 not shown) Planarity restraints: 2705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 703 " 0.295 2.00e-02 2.50e+03 2.50e-01 7.80e+02 pdb=" C7 NAG B 703 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B 703 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG B 703 " -0.429 2.00e-02 2.50e+03 pdb=" O7 NAG B 703 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " -0.238 2.00e-02 2.50e+03 1.92e-01 4.61e+02 pdb=" C7 NAG A 607 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " -0.171 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " 0.305 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 702 " 0.140 2.00e-02 2.50e+03 1.18e-01 1.73e+02 pdb=" C7 NAG F 702 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG F 702 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG F 702 " -0.188 2.00e-02 2.50e+03 pdb=" O7 NAG F 702 " 0.112 2.00e-02 2.50e+03 ... (remaining 2702 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 80 2.58 - 3.16: 12863 3.16 - 3.74: 21756 3.74 - 4.32: 33588 4.32 - 4.90: 52100 Nonbonded interactions: 120387 Sorted by model distance: nonbonded pdb=" O ASN D 80 " pdb=" OD1 ASN D 80 " model vdw 2.004 3.040 nonbonded pdb=" O3 NAG C 601 " pdb=" O7 NAG C 601 " model vdw 2.052 3.040 nonbonded pdb=" O4 NAG C 601 " pdb=" O6 NAG C 601 " model vdw 2.166 3.040 nonbonded pdb=" N HIS F 585 " pdb=" O HIS F 585 " model vdw 2.244 2.496 nonbonded pdb=" OD1 ASN A 137 " pdb=" C1 NAG A 606 " model vdw 2.255 3.470 ... (remaining 120382 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 605) selection = (chain 'C' and resid 33 through 605) selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 519 through 702) selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } ncs_group { reference = (chain 'H' and resid 10 through 116) selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'g' } 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: 3.920 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.690 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.132 16027 Z= 1.193 Angle : 1.775 18.582 21975 Z= 1.090 Chirality : 0.149 0.606 2764 Planarity : 0.011 0.250 2650 Dihedral : 9.941 82.634 5154 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.28 % 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: 0.89 (0.20), residues: 1635 helix: 0.12 (0.23), residues: 423 sheet: 0.88 (0.23), residues: 477 loop : 0.92 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 500 TYR 0.044 0.007 TYR A 40 PHE 0.030 0.005 PHE A 383 TRP 0.060 0.009 TRP C 69 HIS 0.010 0.003 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02194 / 1.16 (15902) covalent geometry : angle 1.72954 / 1.09 (21633) SS BOND : bond 0.01267 / 0.72 ( 33) SS BOND : angle 2.55866 / 1.80 ( 66) hydrogen bonds : bond 0.17249 / 11.27 ( 547) hydrogen bonds : angle 8.01398 / 5.50 ( 1893) link_ALPHA1-3 : bond 0.08561 / 4.28 ( 3) link_ALPHA1-3 : angle 4.32041 / 3.05 ( 9) link_ALPHA1-6 : bond 0.05224 / 2.63 ( 2) link_ALPHA1-6 : angle 2.60905 / 1.94 ( 6) link_BETA1-4 : bond 0.07161 / 4.22 ( 32) link_BETA1-4 : angle 4.84189 / 3.33 ( 96) link_NAG-ASN : bond 0.07515 / 4.94 ( 55) link_NAG-ASN : angle 3.17052 / 2.04 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: D 373 THR cc_start: 0.8943 (t) cc_final: 0.8740 (p) REVERT: F 577 GLN cc_start: 0.8350 (mt0) cc_final: 0.8060 (tt0) REVERT: A 150 MET cc_start: 0.8269 (mmm) cc_final: 0.8040 (mmp) REVERT: A 167 ASP cc_start: 0.8389 (p0) cc_final: 0.8081 (p0) REVERT: A 180 ASP cc_start: 0.7828 (p0) cc_final: 0.7432 (p0) REVERT: A 467 THR cc_start: 0.7868 (m) cc_final: 0.7506 (m) REVERT: B 535 MET cc_start: 0.8243 (mmp) cc_final: 0.7945 (mmp) REVERT: B 622 ILE cc_start: 0.8887 (mt) cc_final: 0.8666 (mt) REVERT: C 161 MET cc_start: 0.8588 (tpt) cc_final: 0.8141 (tpt) REVERT: C 198 THR cc_start: 0.9078 (p) cc_final: 0.8767 (p) REVERT: C 199 SER cc_start: 0.8764 (t) cc_final: 0.8362 (m) REVERT: E 590 GLN cc_start: 0.9277 (mm-40) cc_final: 0.8971 (mm-40) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.1323 time to fit residues: 71.3858 Evaluate side-chains 177 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 HIS D 425 ASN F 607 ASN C 33 ASN C 67 ASN C 195 ASN C 216 HIS C 422 GLN E 570 HIS E 658 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112535 restraints weight = 25890.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115613 restraints weight = 14226.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117617 restraints weight = 9663.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118950 restraints weight = 7469.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119762 restraints weight = 6254.627| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16027 Z= 0.181 Angle : 0.759 12.767 21975 Z= 0.376 Chirality : 0.046 0.235 2764 Planarity : 0.005 0.093 2650 Dihedral : 4.680 19.214 1989 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.14 % Allowed : 7.36 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1635 helix: 1.48 (0.26), residues: 417 sheet: 0.71 (0.24), residues: 411 loop : 0.26 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 178 TYR 0.024 0.002 TYR A 217 PHE 0.013 0.002 PHE D 353 TRP 0.020 0.002 TRP C 112 HIS 0.004 0.001 HIS D 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (15902) covalent geometry : angle 0.70900 / 0.37 (21633) SS BOND : bond 0.00510 / 0.27 ( 33) SS BOND : angle 1.69082 / 1.28 ( 66) hydrogen bonds : bond 0.06400 / 4.28 ( 547) hydrogen bonds : angle 5.72394 / 3.96 ( 1893) link_ALPHA1-3 : bond 0.01334 / 0.66 ( 3) link_ALPHA1-3 : angle 1.37854 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00742 / 0.38 ( 2) link_ALPHA1-6 : angle 1.44541 / 0.95 ( 6) link_BETA1-4 : bond 0.00481 / 0.31 ( 32) link_BETA1-4 : angle 2.24824 / 1.59 ( 96) link_NAG-ASN : bond 0.00402 / 0.25 ( 55) link_NAG-ASN : angle 2.55867 / 1.75 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 373 THR cc_start: 0.8947 (t) cc_final: 0.8604 (p) REVERT: A 150 MET cc_start: 0.8132 (mmm) cc_final: 0.7640 (mmp) REVERT: A 323 ILE cc_start: 0.7685 (mt) cc_final: 0.6890 (mm) REVERT: B 590 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8324 (mm110) REVERT: C 150 MET cc_start: 0.8621 (mmp) cc_final: 0.7888 (mmp) REVERT: C 161 MET cc_start: 0.8481 (tpt) cc_final: 0.8099 (tpt) REVERT: C 199 SER cc_start: 0.8579 (t) cc_final: 0.8231 (m) REVERT: E 590 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8914 (mm-40) REVERT: E 632 ASP cc_start: 0.8986 (t0) cc_final: 0.8753 (t0) outliers start: 32 outliers final: 20 residues processed: 255 average time/residue: 0.1187 time to fit residues: 45.8541 Evaluate side-chains 194 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS C 33 ASN C 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109715 restraints weight = 26203.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112750 restraints weight = 14454.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114706 restraints weight = 9837.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116018 restraints weight = 7620.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116809 restraints weight = 6367.067| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16027 Z= 0.168 Angle : 0.669 11.650 21975 Z= 0.328 Chirality : 0.044 0.228 2764 Planarity : 0.004 0.048 2650 Dihedral : 4.485 25.653 1989 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.48 % Allowed : 8.84 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.77 (0.20), residues: 1635 helix: 1.60 (0.27), residues: 417 sheet: 0.39 (0.23), residues: 453 loop : 0.09 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 308 TYR 0.022 0.001 TYR B 586 PHE 0.012 0.002 PHE E 522 TRP 0.012 0.001 TRP A 96 HIS 0.009 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (15902) covalent geometry : angle 0.63183 / 0.32 (21633) SS BOND : bond 0.00473 / 0.25 ( 33) SS BOND : angle 1.46943 / 1.12 ( 66) hydrogen bonds : bond 0.05417 / 3.64 ( 547) hydrogen bonds : angle 5.16348 / 3.57 ( 1893) link_ALPHA1-3 : bond 0.00999 / 0.50 ( 3) link_ALPHA1-3 : angle 1.40969 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00736 / 0.37 ( 2) link_ALPHA1-6 : angle 1.41764 / 1.04 ( 6) link_BETA1-4 : bond 0.00527 / 0.32 ( 32) link_BETA1-4 : angle 1.64797 / 1.15 ( 96) link_NAG-ASN : bond 0.00264 / 0.18 ( 55) link_NAG-ASN : angle 2.15056 / 1.47 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: D 229 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7525 (ptpt) REVERT: D 373 THR cc_start: 0.9054 (t) cc_final: 0.8796 (p) REVERT: D 434 MET cc_start: 0.8793 (tmm) cc_final: 0.8233 (ttp) REVERT: A 150 MET cc_start: 0.8294 (mmm) cc_final: 0.8071 (mmt) REVERT: A 323 ILE cc_start: 0.7652 (mt) cc_final: 0.6856 (mm) REVERT: B 535 MET cc_start: 0.7732 (mmp) cc_final: 0.7510 (mmp) REVERT: B 648 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6673 (mt-10) REVERT: C 161 MET cc_start: 0.8376 (tpt) cc_final: 0.8087 (tpt) REVERT: C 199 SER cc_start: 0.8422 (t) cc_final: 0.8006 (m) outliers start: 37 outliers final: 25 residues processed: 219 average time/residue: 0.1235 time to fit residues: 41.8629 Evaluate side-chains 184 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 229 LYS Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 183 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 33 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS C 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105899 restraints weight = 26284.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108843 restraints weight = 14661.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110753 restraints weight = 10016.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112020 restraints weight = 7789.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112817 restraints weight = 6561.814| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16027 Z= 0.215 Angle : 0.696 11.108 21975 Z= 0.340 Chirality : 0.045 0.268 2764 Planarity : 0.004 0.048 2650 Dihedral : 4.554 28.710 1989 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.28 % Allowed : 9.30 % Favored : 87.42 % 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: 0.48 (0.20), residues: 1635 helix: 1.48 (0.27), residues: 417 sheet: 0.69 (0.25), residues: 375 loop : -0.41 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 151 TYR 0.015 0.002 TYR B 586 PHE 0.017 0.002 PHE E 522 TRP 0.013 0.002 TRP A 96 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (15902) covalent geometry : angle 0.66601 / 0.33 (21633) SS BOND : bond 0.00411 / 0.24 ( 33) SS BOND : angle 1.30930 / 0.99 ( 66) hydrogen bonds : bond 0.05340 / 3.58 ( 547) hydrogen bonds : angle 5.03167 / 3.49 ( 1893) link_ALPHA1-3 : bond 0.00914 / 0.46 ( 3) link_ALPHA1-3 : angle 1.44639 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00632 / 0.32 ( 2) link_ALPHA1-6 : angle 1.58325 / 1.19 ( 6) link_BETA1-4 : bond 0.00440 / 0.26 ( 32) link_BETA1-4 : angle 1.51183 / 1.04 ( 96) link_NAG-ASN : bond 0.00325 / 0.21 ( 55) link_NAG-ASN : angle 2.05362 / 1.42 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 373 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8828 (p) REVERT: D 434 MET cc_start: 0.8775 (tmm) cc_final: 0.8332 (ttp) REVERT: A 150 MET cc_start: 0.8423 (mmm) cc_final: 0.7994 (mmt) REVERT: A 195 ASN cc_start: 0.9089 (p0) cc_final: 0.8855 (p0) REVERT: B 601 LYS cc_start: 0.9299 (mtpp) cc_final: 0.8745 (mtmm) REVERT: C 199 SER cc_start: 0.8519 (t) cc_final: 0.8021 (m) REVERT: E 633 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8468 (mmtm) outliers start: 49 outliers final: 32 residues processed: 195 average time/residue: 0.1136 time to fit residues: 35.2242 Evaluate side-chains 179 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 40 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 184 optimal weight: 30.0000 chunk 131 optimal weight: 0.8980 chunk 167 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 195 ASN E 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106710 restraints weight = 26159.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109640 restraints weight = 14413.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111554 restraints weight = 9768.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112785 restraints weight = 7541.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113676 restraints weight = 6326.576| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16027 Z= 0.167 Angle : 0.632 10.042 21975 Z= 0.306 Chirality : 0.044 0.252 2764 Planarity : 0.004 0.041 2650 Dihedral : 4.409 27.100 1989 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.68 % Allowed : 10.98 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.20), residues: 1635 helix: 1.51 (0.27), residues: 417 sheet: 0.48 (0.25), residues: 381 loop : -0.51 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 298 TYR 0.023 0.001 TYR A 173 PHE 0.012 0.001 PHE E 522 TRP 0.025 0.001 TRP E 571 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (15902) covalent geometry : angle 0.60101 / 0.30 (21633) SS BOND : bond 0.00434 / 0.23 ( 33) SS BOND : angle 1.37549 / 1.02 ( 66) hydrogen bonds : bond 0.04846 / 3.25 ( 547) hydrogen bonds : angle 4.83418 / 3.36 ( 1893) link_ALPHA1-3 : bond 0.00936 / 0.47 ( 3) link_ALPHA1-3 : angle 1.43249 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00602 / 0.30 ( 2) link_ALPHA1-6 : angle 1.52900 / 1.12 ( 6) link_BETA1-4 : bond 0.00406 / 0.25 ( 32) link_BETA1-4 : angle 1.34508 / 0.92 ( 96) link_NAG-ASN : bond 0.00230 / 0.15 ( 55) link_NAG-ASN : angle 1.95932 / 1.34 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 199 SER cc_start: 0.8947 (p) cc_final: 0.8726 (m) REVERT: D 373 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8823 (p) REVERT: D 434 MET cc_start: 0.8765 (tmm) cc_final: 0.8278 (ttp) REVERT: A 150 MET cc_start: 0.8052 (mmm) cc_final: 0.7452 (mmp) REVERT: B 601 LYS cc_start: 0.9297 (mtpp) cc_final: 0.8739 (mtmm) REVERT: C 199 SER cc_start: 0.8422 (t) cc_final: 0.7896 (m) REVERT: E 571 TRP cc_start: 0.6476 (m100) cc_final: 0.6005 (m100) REVERT: E 622 ILE cc_start: 0.8923 (mt) cc_final: 0.8669 (mt) REVERT: E 633 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8391 (mmtm) outliers start: 40 outliers final: 30 residues processed: 199 average time/residue: 0.1168 time to fit residues: 36.4783 Evaluate side-chains 184 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 633 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 19 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 195 ASN C 425 ASN E 570 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102745 restraints weight = 26779.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105381 restraints weight = 15141.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107158 restraints weight = 10508.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108304 restraints weight = 8189.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109081 restraints weight = 6914.884| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16027 Z= 0.216 Angle : 0.682 10.157 21975 Z= 0.329 Chirality : 0.045 0.204 2764 Planarity : 0.004 0.041 2650 Dihedral : 4.488 28.022 1989 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.35 % Allowed : 10.84 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1635 helix: 1.44 (0.27), residues: 417 sheet: 0.42 (0.25), residues: 381 loop : -0.71 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 542 TYR 0.020 0.002 TYR A 173 PHE 0.014 0.002 PHE E 522 TRP 0.018 0.001 TRP E 571 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (15902) covalent geometry : angle 0.65219 / 0.32 (21633) SS BOND : bond 0.00460 / 0.26 ( 33) SS BOND : angle 1.40168 / 1.04 ( 66) hydrogen bonds : bond 0.05058 / 3.37 ( 547) hydrogen bonds : angle 4.89661 / 3.41 ( 1893) link_ALPHA1-3 : bond 0.00958 / 0.48 ( 3) link_ALPHA1-3 : angle 1.46862 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00578 / 0.30 ( 2) link_ALPHA1-6 : angle 1.60032 / 1.21 ( 6) link_BETA1-4 : bond 0.00419 / 0.26 ( 32) link_BETA1-4 : angle 1.40442 / 0.95 ( 96) link_NAG-ASN : bond 0.00305 / 0.20 ( 55) link_NAG-ASN : angle 2.00767 / 1.39 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 199 SER cc_start: 0.9008 (p) cc_final: 0.8781 (m) REVERT: D 373 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8876 (p) REVERT: D 434 MET cc_start: 0.8784 (tmm) cc_final: 0.8364 (ttp) REVERT: A 323 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7177 (mt) REVERT: B 601 LYS cc_start: 0.9329 (mtpp) cc_final: 0.8857 (mtmm) REVERT: C 199 SER cc_start: 0.8569 (t) cc_final: 0.8003 (m) REVERT: E 545 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7948 (tt) REVERT: E 571 TRP cc_start: 0.6795 (m100) cc_final: 0.6389 (m-10) REVERT: E 633 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8420 (mmtm) outliers start: 50 outliers final: 36 residues processed: 198 average time/residue: 0.1090 time to fit residues: 34.9732 Evaluate side-chains 189 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 65 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN C 33 ASN C 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101394 restraints weight = 26916.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104053 restraints weight = 15378.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105802 restraints weight = 10695.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106945 restraints weight = 8393.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107721 restraints weight = 7117.104| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16027 Z= 0.246 Angle : 0.721 12.273 21975 Z= 0.346 Chirality : 0.047 0.320 2764 Planarity : 0.004 0.075 2650 Dihedral : 4.619 31.051 1989 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.21 % Allowed : 12.18 % Favored : 84.61 % 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: -0.02 (0.20), residues: 1635 helix: 1.40 (0.27), residues: 414 sheet: 0.15 (0.25), residues: 405 loop : -0.82 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 542 TYR 0.018 0.002 TYR A 173 PHE 0.015 0.002 PHE E 522 TRP 0.015 0.002 TRP B 571 HIS 0.011 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (15902) covalent geometry : angle 0.69200 / 0.34 (21633) SS BOND : bond 0.00554 / 0.32 ( 33) SS BOND : angle 1.32948 / 1.05 ( 66) hydrogen bonds : bond 0.05226 / 3.48 ( 547) hydrogen bonds : angle 4.97579 / 3.46 ( 1893) link_ALPHA1-3 : bond 0.00945 / 0.47 ( 3) link_ALPHA1-3 : angle 1.51361 / 1.02 ( 9) link_ALPHA1-6 : bond 0.00548 / 0.28 ( 2) link_ALPHA1-6 : angle 1.64211 / 1.25 ( 6) link_BETA1-4 : bond 0.00425 / 0.26 ( 32) link_BETA1-4 : angle 1.42669 / 0.96 ( 96) link_NAG-ASN : bond 0.00344 / 0.22 ( 55) link_NAG-ASN : angle 2.08974 / 1.45 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 199 SER cc_start: 0.9120 (p) cc_final: 0.8910 (m) REVERT: D 373 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8875 (p) REVERT: D 434 MET cc_start: 0.8788 (tmm) cc_final: 0.8381 (ttp) REVERT: A 150 MET cc_start: 0.7969 (mmm) cc_final: 0.7740 (mmt) REVERT: A 323 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7227 (mt) REVERT: B 601 LYS cc_start: 0.9337 (mtpp) cc_final: 0.8862 (mtmm) REVERT: C 199 SER cc_start: 0.8597 (t) cc_final: 0.7993 (m) REVERT: E 571 TRP cc_start: 0.7263 (m100) cc_final: 0.6800 (m-10) REVERT: E 633 LYS cc_start: 0.8638 (mttm) cc_final: 0.8370 (mmtm) outliers start: 48 outliers final: 41 residues processed: 195 average time/residue: 0.1122 time to fit residues: 35.0852 Evaluate side-chains 193 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 152 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 165 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 chunk 179 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 195 ASN E 570 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105096 restraints weight = 26627.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107794 restraints weight = 14970.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109561 restraints weight = 10270.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110646 restraints weight = 7985.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111462 restraints weight = 6766.660| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16027 Z= 0.126 Angle : 0.613 10.338 21975 Z= 0.295 Chirality : 0.043 0.310 2764 Planarity : 0.004 0.040 2650 Dihedral : 4.298 25.149 1989 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.81 % Allowed : 12.99 % Favored : 84.20 % 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: 0.17 (0.20), residues: 1635 helix: 1.64 (0.27), residues: 414 sheet: 0.19 (0.24), residues: 417 loop : -0.73 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 542 TYR 0.019 0.001 TYR A 173 PHE 0.009 0.001 PHE D 376 TRP 0.021 0.001 TRP B 571 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (15902) covalent geometry : angle 0.58524 / 0.29 (21633) SS BOND : bond 0.00412 / 0.22 ( 33) SS BOND : angle 1.19803 / 0.90 ( 66) hydrogen bonds : bond 0.04434 / 2.97 ( 547) hydrogen bonds : angle 4.67571 / 3.26 ( 1893) link_ALPHA1-3 : bond 0.00939 / 0.47 ( 3) link_ALPHA1-3 : angle 1.42395 / 0.98 ( 9) link_ALPHA1-6 : bond 0.00506 / 0.25 ( 2) link_ALPHA1-6 : angle 1.45899 / 1.03 ( 6) link_BETA1-4 : bond 0.00397 / 0.24 ( 32) link_BETA1-4 : angle 1.23346 / 0.84 ( 96) link_NAG-ASN : bond 0.00221 / 0.15 ( 55) link_NAG-ASN : angle 1.87151 / 1.28 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 199 SER cc_start: 0.9113 (p) cc_final: 0.8899 (m) REVERT: D 373 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8815 (p) REVERT: D 434 MET cc_start: 0.8702 (tmm) cc_final: 0.8311 (ttp) REVERT: A 150 MET cc_start: 0.7810 (mmm) cc_final: 0.7550 (mmt) REVERT: B 601 LYS cc_start: 0.9315 (mtpp) cc_final: 0.8851 (mtmm) REVERT: C 154 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8708 (tp) REVERT: C 199 SER cc_start: 0.8523 (t) cc_final: 0.7931 (m) REVERT: E 633 LYS cc_start: 0.8591 (mttm) cc_final: 0.8361 (mmtm) outliers start: 42 outliers final: 32 residues processed: 204 average time/residue: 0.1131 time to fit residues: 36.7704 Evaluate side-chains 188 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 63 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 183 optimal weight: 30.0000 chunk 89 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS C 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102686 restraints weight = 26615.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105392 restraints weight = 15063.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107177 restraints weight = 10398.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108340 restraints weight = 8094.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109095 restraints weight = 6841.856| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16027 Z= 0.178 Angle : 0.642 9.539 21975 Z= 0.310 Chirality : 0.044 0.303 2764 Planarity : 0.004 0.054 2650 Dihedral : 4.337 26.684 1989 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.88 % Allowed : 13.72 % Favored : 83.40 % 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: 0.12 (0.20), residues: 1635 helix: 1.61 (0.27), residues: 414 sheet: 0.20 (0.24), residues: 417 loop : -0.78 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 542 TYR 0.023 0.002 TYR A 173 PHE 0.012 0.001 PHE E 522 TRP 0.015 0.001 TRP B 571 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (15902) covalent geometry : angle 0.61425 / 0.30 (21633) SS BOND : bond 0.00445 / 0.24 ( 33) SS BOND : angle 1.28848 / 0.95 ( 66) hydrogen bonds : bond 0.04675 / 3.13 ( 547) hydrogen bonds : angle 4.74234 / 3.30 ( 1893) link_ALPHA1-3 : bond 0.00966 / 0.48 ( 3) link_ALPHA1-3 : angle 1.47633 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00538 / 0.28 ( 2) link_ALPHA1-6 : angle 1.53613 / 1.14 ( 6) link_BETA1-4 : bond 0.00398 / 0.24 ( 32) link_BETA1-4 : angle 1.30829 / 0.88 ( 96) link_NAG-ASN : bond 0.00263 / 0.17 ( 55) link_NAG-ASN : angle 1.89775 / 1.30 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.572 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: D 199 SER cc_start: 0.9193 (p) cc_final: 0.8915 (m) REVERT: D 373 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8861 (p) REVERT: D 434 MET cc_start: 0.8736 (tmm) cc_final: 0.8322 (ttp) REVERT: A 150 MET cc_start: 0.7908 (mmm) cc_final: 0.7651 (mmt) REVERT: B 601 LYS cc_start: 0.9337 (mtpp) cc_final: 0.8836 (mtmm) REVERT: C 154 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8710 (tp) REVERT: C 199 SER cc_start: 0.8598 (t) cc_final: 0.7975 (m) REVERT: E 633 LYS cc_start: 0.8618 (mttm) cc_final: 0.8368 (mmtm) outliers start: 43 outliers final: 35 residues processed: 185 average time/residue: 0.1147 time to fit residues: 33.5146 Evaluate side-chains 188 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain E residue 663 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 120 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN C 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105484 restraints weight = 26316.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108185 restraints weight = 14730.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110022 restraints weight = 10138.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.111217 restraints weight = 7840.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112011 restraints weight = 6559.591| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16027 Z= 0.117 Angle : 0.580 9.092 21975 Z= 0.281 Chirality : 0.042 0.308 2764 Planarity : 0.004 0.040 2650 Dihedral : 4.123 23.061 1989 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.94 % Allowed : 14.79 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1635 helix: 1.69 (0.27), residues: 417 sheet: 0.28 (0.24), residues: 417 loop : -0.73 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 542 TYR 0.023 0.001 TYR A 173 PHE 0.007 0.001 PHE D 53 TRP 0.015 0.001 TRP B 571 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15902) covalent geometry : angle 0.55362 / 0.28 (21633) SS BOND : bond 0.00383 / 0.20 ( 33) SS BOND : angle 1.15766 / 0.86 ( 66) hydrogen bonds : bond 0.04117 / 2.76 ( 547) hydrogen bonds : angle 4.53392 / 3.16 ( 1893) link_ALPHA1-3 : bond 0.01052 / 0.53 ( 3) link_ALPHA1-3 : angle 1.47322 / 1.02 ( 9) link_ALPHA1-6 : bond 0.00501 / 0.25 ( 2) link_ALPHA1-6 : angle 1.47517 / 1.03 ( 6) link_BETA1-4 : bond 0.00384 / 0.23 ( 32) link_BETA1-4 : angle 1.18532 / 0.81 ( 96) link_NAG-ASN : bond 0.00207 / 0.15 ( 55) link_NAG-ASN : angle 1.75624 / 1.19 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 199 SER cc_start: 0.9181 (p) cc_final: 0.8902 (m) REVERT: D 373 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8804 (p) REVERT: D 434 MET cc_start: 0.8667 (tmm) cc_final: 0.8265 (ttp) REVERT: A 150 MET cc_start: 0.7710 (mmm) cc_final: 0.7444 (mmt) REVERT: B 601 LYS cc_start: 0.9290 (mtpp) cc_final: 0.8821 (mtmm) REVERT: C 199 SER cc_start: 0.8498 (t) cc_final: 0.7923 (m) REVERT: E 571 TRP cc_start: 0.7168 (m100) cc_final: 0.6914 (m-10) REVERT: E 633 LYS cc_start: 0.8536 (mttm) cc_final: 0.8309 (mmtm) outliers start: 29 outliers final: 26 residues processed: 192 average time/residue: 0.1211 time to fit residues: 36.0700 Evaluate side-chains 186 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain E residue 626 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 173 optimal weight: 30.0000 chunk 70 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106228 restraints weight = 26449.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108933 restraints weight = 14834.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110736 restraints weight = 10172.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111871 restraints weight = 7868.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112609 restraints weight = 6628.047| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.221 16027 Z= 0.197 Angle : 0.784 59.135 21975 Z= 0.426 Chirality : 0.046 0.841 2764 Planarity : 0.004 0.040 2650 Dihedral : 4.124 23.154 1989 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.01 % Allowed : 14.52 % Favored : 83.47 % 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: 0.23 (0.20), residues: 1635 helix: 1.68 (0.27), residues: 417 sheet: 0.28 (0.24), residues: 417 loop : -0.73 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 178 TYR 0.021 0.001 TYR A 173 PHE 0.007 0.001 PHE D 53 TRP 0.013 0.001 TRP C 112 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (15902) covalent geometry : angle 0.76424 / 0.42 (21633) SS BOND : bond 0.00921 / 0.56 ( 33) SS BOND : angle 1.76897 / 1.50 ( 66) hydrogen bonds : bond 0.04152 / 2.79 ( 547) hydrogen bonds : angle 4.53389 / 3.16 ( 1893) link_ALPHA1-3 : bond 0.00809 / 0.40 ( 3) link_ALPHA1-3 : angle 1.39692 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00480 / 0.24 ( 2) link_ALPHA1-6 : angle 1.46500 / 1.03 ( 6) link_BETA1-4 : bond 0.00408 / 0.25 ( 32) link_BETA1-4 : angle 1.18349 / 0.81 ( 96) link_NAG-ASN : bond 0.00212 / 0.15 ( 55) link_NAG-ASN : angle 1.75363 / 1.19 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.25 seconds wall clock time: 43 minutes 14.98 seconds (2594.98 seconds total)