Starting phenix.real_space_refine on Wed Mar 4 09:06:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sgf_25109/03_2026/7sgf_25109.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgf_25109/03_2026/7sgf_25109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sgf_25109/03_2026/7sgf_25109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgf_25109/03_2026/7sgf_25109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sgf_25109/03_2026/7sgf_25109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgf_25109/03_2026/7sgf_25109.map" } resolution = 4.41 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= 0.001 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 90 5.16 5 C 7404 2.51 5 N 2031 2.21 5 O 2553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12078 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "a" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'PHE:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 8, 'TRP:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "L" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 2, 'PHE:plan': 4, 'TRP:plan': 1, 'TYR:plan': 4, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "b" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "J" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'PHE:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 8, 'TRP:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "K" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 2, 'PHE:plan': 4, 'TRP:plan': 1, 'TYR:plan': 4, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 145 Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "c" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "M" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'PHE:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 8, 'TRP:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "N" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 2, 'PHE:plan': 4, 'TRP:plan': 1, 'TYR:plan': 4, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 145 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "l" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.17, per 1000 atoms: 0.26 Number of scatterers: 12078 At special positions: 0 Unit cell: (143.17, 135.96, 95.79, 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 90 16.00 O 2553 8.00 N 2031 7.00 C 7404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.08 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.01 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.04 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.08 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.01 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.04 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.04 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.08 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.01 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.04 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " 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 F 3 " - " MAN F 4 " " BMA U 3 " - " MAN U 4 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA U 3 " - " MAN U 5 " " BMA g 3 " - " MAN g 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG 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 i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " BETA1-6 " NAG P 1 " - " FUC P 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG Y 1 " - " FUC Y 4 " " NAG Z 1 " - " FUC Z 3 " " NAG k 1 " - " FUC k 4 " " NAG l 1 " - " FUC l 3 " NAG-ASN " NAG A 701 " - " ASN A 99 " " NAG A 702 " - " ASN A 224 " " NAG B 701 " - " ASN B 99 " " NAG B 702 " - " ASN B 224 " " NAG C 701 " - " ASN C 99 " " NAG C 702 " - " ASN C 224 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 109 " " NAG G 1 " - " ASN A 119 " " NAG I 1 " - " ASN A 167 " " NAG O 1 " - " ASN a 373 " " NAG P 1 " - " ASN a 390 " " NAG Q 1 " - " ASN a 395 " " NAG R 1 " - " ASN a 365 " " NAG S 1 " - " ASN B 79 " " NAG T 1 " - " ASN B 89 " " NAG U 1 " - " ASN B 109 " " NAG V 1 " - " ASN B 119 " " NAG W 1 " - " ASN B 167 " " NAG X 1 " - " ASN b 373 " " NAG Y 1 " - " ASN b 390 " " NAG Z 1 " - " ASN b 395 " " NAG d 1 " - " ASN b 365 " " NAG e 1 " - " ASN C 79 " " NAG f 1 " - " ASN C 89 " " NAG g 1 " - " ASN C 109 " " NAG h 1 " - " ASN C 119 " " NAG i 1 " - " ASN C 167 " " NAG j 1 " - " ASN c 373 " " NAG k 1 " - " ASN c 390 " " NAG l 1 " - " ASN c 395 " " NAG m 1 " - " ASN c 365 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 467.1 milliseconds 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 27 sheets defined 23.9% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'a' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 345 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.539A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 415 Processing helix chain 'H' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP H 67 " --> pdb=" O TRP H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'b' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL b 298 " --> pdb=" O GLY b 294 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 345 Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.538A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 415 Processing helix chain 'J' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP J 67 " --> pdb=" O TRP J 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 64 through 67' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'c' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL c 298 " --> pdb=" O GLY c 294 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 345 Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.538A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 415 Processing helix chain 'M' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP M 67 " --> pdb=" O TRP M 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 64 through 67' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 4.441A pdb=" N ASN a 365 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP a 386 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER a 367 " --> pdb=" O LYS a 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS a 384 " --> pdb=" O SER a 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY H 16 " --> pdb=" O GLY H 85 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR H 78 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR H 74 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR H 80 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER H 72 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN H 82 " --> pdb=" O SER H 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.287A pdb=" N CYS H 96 " --> pdb=" O TRP H 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP H 116 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS H 98 " --> pdb=" O ASP H 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.567A pdb=" N ARG H 109 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL L 11 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 62 removed outlier: 4.441A pdb=" N ASN b 365 " --> pdb=" O TRP b 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP b 386 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER b 367 " --> pdb=" O LYS b 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS b 384 " --> pdb=" O SER b 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AB4, first strand: chain 'J' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY J 16 " --> pdb=" O GLY J 85 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR J 78 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR J 74 " --> pdb=" O THR J 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR J 80 " --> pdb=" O SER J 72 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER J 72 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN J 82 " --> pdb=" O SER J 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG J 39 " --> pdb=" O TRP J 48 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TRP J 48 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.287A pdb=" N CYS J 96 " --> pdb=" O TRP J 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP J 116 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS J 98 " --> pdb=" O ASP J 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 102 through 103 removed outlier: 3.567A pdb=" N ARG J 109 " --> pdb=" O ARG J 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL K 11 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AC2, first strand: chain 'C' and resid 61 through 62 removed outlier: 4.441A pdb=" N ASN c 365 " --> pdb=" O TRP c 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP c 386 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER c 367 " --> pdb=" O LYS c 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS c 384 " --> pdb=" O SER c 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AC4, first strand: chain 'M' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY M 16 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR M 78 " --> pdb=" O THR M 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR M 74 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR M 80 " --> pdb=" O SER M 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER M 72 " --> pdb=" O THR M 80 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN M 82 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG M 39 " --> pdb=" O TRP M 48 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TRP M 48 " --> pdb=" O ARG M 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.286A pdb=" N CYS M 96 " --> pdb=" O TRP M 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP M 116 " --> pdb=" O CYS M 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS M 98 " --> pdb=" O ASP M 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 102 through 103 removed outlier: 3.568A pdb=" N ARG M 109 " --> pdb=" O ARG M 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL N 11 " --> pdb=" O VAL N 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN N 39 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1458 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: 2.62 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3101 1.33 - 1.47: 3750 1.47 - 1.60: 5224 1.60 - 1.74: 24 1.74 - 1.88: 132 Bond restraints: 12231 Sorted by residual: bond pdb=" CB TYR C 94 " pdb=" CG TYR C 94 " ideal model delta sigma weight residual 1.512 1.390 0.122 2.20e-02 2.07e+03 3.06e+01 bond pdb=" CB TYR A 94 " pdb=" CG TYR A 94 " ideal model delta sigma weight residual 1.512 1.390 0.122 2.20e-02 2.07e+03 3.06e+01 bond pdb=" CB TYR B 94 " pdb=" CG TYR B 94 " ideal model delta sigma weight residual 1.512 1.391 0.121 2.20e-02 2.07e+03 3.05e+01 bond pdb=" CB LEU a 415 " pdb=" CG LEU a 415 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" CB LEU b 415 " pdb=" CG LEU b 415 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 12226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13416 2.38 - 4.77: 2660 4.77 - 7.15: 458 7.15 - 9.54: 87 9.54 - 11.92: 29 Bond angle restraints: 16650 Sorted by residual: angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 112.90 121.94 -9.04 9.60e-01 1.09e+00 8.86e+01 angle pdb=" N VAL B 65 " pdb=" CA VAL B 65 " pdb=" C VAL B 65 " ideal model delta sigma weight residual 112.90 121.92 -9.02 9.60e-01 1.09e+00 8.84e+01 angle pdb=" N VAL C 65 " pdb=" CA VAL C 65 " pdb=" C VAL C 65 " ideal model delta sigma weight residual 112.90 121.92 -9.02 9.60e-01 1.09e+00 8.83e+01 angle pdb=" N PHE M 104 " pdb=" CA PHE M 104 " pdb=" C PHE M 104 " ideal model delta sigma weight residual 112.92 124.32 -11.40 1.23e+00 6.61e-01 8.59e+01 angle pdb=" N PHE J 104 " pdb=" CA PHE J 104 " pdb=" C PHE J 104 " ideal model delta sigma weight residual 112.92 124.31 -11.39 1.23e+00 6.61e-01 8.58e+01 ... (remaining 16645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 7881 21.23 - 42.46: 240 42.46 - 63.69: 36 63.69 - 84.92: 87 84.92 - 106.16: 75 Dihedral angle restraints: 8319 sinusoidal: 3639 harmonic: 4680 Sorted by residual: dihedral pdb=" CB CYS a 301 " pdb=" SG CYS a 301 " pdb=" SG CYS a 310 " pdb=" CB CYS a 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.62 85.62 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS c 301 " pdb=" SG CYS c 301 " pdb=" SG CYS c 310 " pdb=" CB CYS c 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.62 85.62 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS b 301 " pdb=" SG CYS b 301 " pdb=" SG CYS b 310 " pdb=" CB CYS b 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.60 85.60 1 1.00e+01 1.00e-02 8.86e+01 ... (remaining 8316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1390 0.105 - 0.209: 495 0.209 - 0.314: 186 0.314 - 0.418: 71 0.418 - 0.523: 60 Chirality restraints: 2202 Sorted by residual: chirality pdb=" C1 BMA e 3 " pdb=" O4 NAG e 2 " pdb=" C2 BMA e 3 " pdb=" O5 BMA e 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 2199 not shown) Planarity restraints: 2103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.82e+02 pdb=" C7 NAG W 1 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.82e+02 pdb=" C7 NAG i 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.81e+02 pdb=" C7 NAG I 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.020 2.00e-02 2.50e+03 ... (remaining 2100 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4235 2.86 - 3.37: 11353 3.37 - 3.88: 19394 3.88 - 4.39: 22062 4.39 - 4.90: 34281 Nonbonded interactions: 91325 Sorted by model distance: nonbonded pdb=" O3 NAG S 2 " pdb=" O7 NAG S 2 " model vdw 2.354 3.040 nonbonded pdb=" O3 NAG D 2 " pdb=" O7 NAG D 2 " model vdw 2.355 3.040 nonbonded pdb=" O3 NAG e 2 " pdb=" O7 NAG e 2 " model vdw 2.355 3.040 nonbonded pdb=" N TYR C 200 " pdb=" N ILE C 201 " model vdw 2.381 2.560 nonbonded pdb=" N TYR B 200 " pdb=" N ILE B 201 " model vdw 2.382 2.560 ... (remaining 91320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'O' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'f' selection = chain 'h' selection = chain 'j' } ncs_group { reference = chain 'F' selection = chain 'U' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 4.550 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.300 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.149 12339 Z= 1.225 Angle : 2.116 13.698 16953 Z= 1.328 Chirality : 0.151 0.523 2202 Planarity : 0.014 0.250 2070 Dihedral : 17.976 106.156 5244 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.03 (0.19), residues: 1605 helix: 0.11 (0.24), residues: 315 sheet: 0.86 (0.27), residues: 333 loop : -0.33 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG c 314 TYR 0.079 0.010 TYR b 363 PHE 0.031 0.006 PHE b 309 TRP 0.037 0.008 TRP a 370 HIS 0.008 0.002 HIS a 354 Details of bonding type rmsd covalent geometry : bond 0.02183 (12231) covalent geometry : angle 2.04419 (16650) SS BOND : bond 0.01984 ( 21) SS BOND : angle 3.06152 ( 42) hydrogen bonds : bond 0.16954 ( 531) hydrogen bonds : angle 8.18612 ( 1458) link_ALPHA1-3 : bond 0.08879 ( 3) link_ALPHA1-3 : angle 7.95870 ( 9) link_ALPHA1-6 : bond 0.06533 ( 3) link_ALPHA1-6 : angle 2.34277 ( 9) link_BETA1-4 : bond 0.06311 ( 42) link_BETA1-4 : angle 5.06774 ( 126) link_BETA1-6 : bond 0.06288 ( 6) link_BETA1-6 : angle 7.27622 ( 18) link_NAG-ASN : bond 0.07030 ( 33) link_NAG-ASN : angle 3.35269 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.6735 (mttt) cc_final: 0.6480 (mmtt) REVERT: A 144 ILE cc_start: 0.8021 (mt) cc_final: 0.7700 (mt) REVERT: A 200 TYR cc_start: 0.8807 (p90) cc_final: 0.8545 (p90) REVERT: A 217 TYR cc_start: 0.7930 (m-80) cc_final: 0.6915 (m-80) REVERT: A 227 TRP cc_start: 0.7889 (p90) cc_final: 0.7246 (p-90) REVERT: A 228 GLU cc_start: 0.8290 (pm20) cc_final: 0.7974 (pp20) REVERT: A 236 PRO cc_start: 0.8505 (Cg_endo) cc_final: 0.7927 (Cg_exo) REVERT: a 308 GLU cc_start: 0.8539 (mp0) cc_final: 0.8275 (mm-30) REVERT: a 371 TYR cc_start: 0.7382 (m-80) cc_final: 0.7112 (m-80) REVERT: a 396 GLU cc_start: 0.8773 (mp0) cc_final: 0.8567 (mp0) REVERT: B 144 ILE cc_start: 0.8029 (mt) cc_final: 0.7745 (mt) REVERT: B 217 TYR cc_start: 0.7811 (m-80) cc_final: 0.6836 (m-80) REVERT: B 227 TRP cc_start: 0.7911 (p90) cc_final: 0.7377 (p-90) REVERT: B 228 GLU cc_start: 0.8067 (pm20) cc_final: 0.7751 (pp20) REVERT: B 236 PRO cc_start: 0.8579 (Cg_endo) cc_final: 0.8049 (Cg_exo) REVERT: b 311 ASP cc_start: 0.8674 (m-30) cc_final: 0.8206 (t0) REVERT: b 371 TYR cc_start: 0.7389 (m-80) cc_final: 0.7026 (m-80) REVERT: b 396 GLU cc_start: 0.8700 (mp0) cc_final: 0.8469 (mp0) REVERT: C 78 LEU cc_start: 0.8753 (mt) cc_final: 0.8468 (mp) REVERT: C 144 ILE cc_start: 0.8057 (mt) cc_final: 0.7750 (mt) REVERT: C 211 ASP cc_start: 0.8000 (p0) cc_final: 0.7610 (p0) REVERT: C 217 TYR cc_start: 0.7983 (m-80) cc_final: 0.7077 (m-80) REVERT: C 236 PRO cc_start: 0.8575 (Cg_endo) cc_final: 0.7968 (Cg_exo) REVERT: c 311 ASP cc_start: 0.8598 (m-30) cc_final: 0.8213 (t0) REVERT: c 316 PHE cc_start: 0.8584 (m-80) cc_final: 0.8190 (m-10) REVERT: c 321 GLN cc_start: 0.8332 (mt0) cc_final: 0.7941 (mm-40) REVERT: c 396 GLU cc_start: 0.8699 (mp0) cc_final: 0.8498 (mp0) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1204 time to fit residues: 59.6234 Evaluate side-chains 188 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 141 HIS A 218 GLN a 331 GLN B 92 HIS b 321 GLN b 338 ASN b 405 GLN C 92 HIS C 141 HIS C 218 GLN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.076853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.065506 restraints weight = 80793.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.066889 restraints weight = 54992.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.067832 restraints weight = 41379.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.068546 restraints weight = 33679.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.068932 restraints weight = 29020.753| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12339 Z= 0.246 Angle : 1.022 12.178 16953 Z= 0.489 Chirality : 0.054 0.342 2202 Planarity : 0.004 0.036 2070 Dihedral : 15.284 102.838 3450 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.70 % Allowed : 4.91 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1605 helix: 0.61 (0.27), residues: 345 sheet: 0.73 (0.29), residues: 318 loop : -0.67 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 325 TYR 0.029 0.003 TYR B 66 PHE 0.025 0.002 PHE A 233 TRP 0.012 0.002 TRP c 370 HIS 0.011 0.002 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00503 (12231) covalent geometry : angle 0.94008 (16650) SS BOND : bond 0.00527 ( 21) SS BOND : angle 1.31443 ( 42) hydrogen bonds : bond 0.05821 ( 531) hydrogen bonds : angle 6.12079 ( 1458) link_ALPHA1-3 : bond 0.01244 ( 3) link_ALPHA1-3 : angle 4.68238 ( 9) link_ALPHA1-6 : bond 0.02044 ( 3) link_ALPHA1-6 : angle 1.33361 ( 9) link_BETA1-4 : bond 0.00866 ( 42) link_BETA1-4 : angle 3.22322 ( 126) link_BETA1-6 : bond 0.03323 ( 6) link_BETA1-6 : angle 6.08469 ( 18) link_NAG-ASN : bond 0.00990 ( 33) link_NAG-ASN : angle 2.71678 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 255 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8286 (mp0) cc_final: 0.8069 (mp0) REVERT: A 80 MET cc_start: 0.8552 (mtm) cc_final: 0.8319 (mtm) REVERT: A 130 ASP cc_start: 0.8635 (m-30) cc_final: 0.8354 (m-30) REVERT: A 200 TYR cc_start: 0.8240 (p90) cc_final: 0.7955 (p90) REVERT: A 205 SER cc_start: 0.8427 (p) cc_final: 0.8215 (t) REVERT: A 217 TYR cc_start: 0.7254 (m-80) cc_final: 0.6998 (m-80) REVERT: A 218 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6162 (tm-30) REVERT: A 228 GLU cc_start: 0.8446 (pm20) cc_final: 0.7746 (pp20) REVERT: A 236 PRO cc_start: 0.8894 (Cg_endo) cc_final: 0.8271 (Cg_exo) REVERT: a 363 TYR cc_start: 0.7360 (p90) cc_final: 0.7061 (p90) REVERT: a 371 TYR cc_start: 0.6663 (m-80) cc_final: 0.6276 (m-80) REVERT: a 396 GLU cc_start: 0.8597 (mp0) cc_final: 0.8260 (mp0) REVERT: a 408 ASP cc_start: 0.7702 (t0) cc_final: 0.7449 (t70) REVERT: a 410 MET cc_start: 0.9047 (mtt) cc_final: 0.8804 (mtp) REVERT: B 100 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8321 (mm-30) REVERT: B 130 ASP cc_start: 0.8381 (m-30) cc_final: 0.8169 (m-30) REVERT: B 200 TYR cc_start: 0.8200 (p90) cc_final: 0.7979 (p90) REVERT: B 205 SER cc_start: 0.8545 (p) cc_final: 0.8299 (t) REVERT: B 217 TYR cc_start: 0.7288 (m-80) cc_final: 0.7020 (m-80) REVERT: B 228 GLU cc_start: 0.8296 (pm20) cc_final: 0.7866 (pp20) REVERT: B 236 PRO cc_start: 0.9126 (Cg_endo) cc_final: 0.8417 (Cg_exo) REVERT: b 335 GLN cc_start: 0.8972 (pm20) cc_final: 0.8621 (pm20) REVERT: b 336 LEU cc_start: 0.9079 (tp) cc_final: 0.8845 (tp) REVERT: b 396 GLU cc_start: 0.8597 (mp0) cc_final: 0.8126 (mp0) REVERT: b 410 MET cc_start: 0.9250 (mtt) cc_final: 0.9000 (mtp) REVERT: C 100 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8115 (mm-30) REVERT: C 116 LYS cc_start: 0.8041 (mttt) cc_final: 0.7455 (tptt) REVERT: C 134 MET cc_start: 0.7159 (ttp) cc_final: 0.5374 (mtt) REVERT: C 156 ASP cc_start: 0.6933 (t0) cc_final: 0.6253 (t70) REVERT: C 161 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8188 (pttt) REVERT: C 189 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8477 (tp40) REVERT: C 205 SER cc_start: 0.8494 (p) cc_final: 0.8281 (t) REVERT: C 236 PRO cc_start: 0.8929 (Cg_endo) cc_final: 0.8220 (Cg_exo) REVERT: c 316 PHE cc_start: 0.8580 (m-80) cc_final: 0.8331 (m-80) REVERT: c 321 GLN cc_start: 0.8332 (mt0) cc_final: 0.7789 (mm-40) REVERT: c 396 GLU cc_start: 0.8655 (mp0) cc_final: 0.8434 (mp0) REVERT: c 408 ASP cc_start: 0.7780 (t0) cc_final: 0.7574 (t70) REVERT: c 410 MET cc_start: 0.9031 (mtt) cc_final: 0.8739 (mtp) outliers start: 6 outliers final: 2 residues processed: 259 average time/residue: 0.1054 time to fit residues: 39.2338 Evaluate side-chains 183 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 180 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 148 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 99 optimal weight: 50.0000 chunk 56 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 150 optimal weight: 30.0000 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 331 GLN a 374 HIS ** a 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS b 331 GLN b 338 ASN b 374 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 331 GLN c 374 HIS ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.073632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.062512 restraints weight = 82376.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063782 restraints weight = 55981.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.064701 restraints weight = 42418.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.065382 restraints weight = 34836.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.065835 restraints weight = 30048.036| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 12339 Z= 0.283 Angle : 1.033 13.185 16953 Z= 0.492 Chirality : 0.052 0.351 2202 Planarity : 0.005 0.049 2070 Dihedral : 12.698 95.869 3450 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.82 % Allowed : 7.02 % Favored : 92.16 % 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: -0.65 (0.20), residues: 1605 helix: 0.44 (0.29), residues: 339 sheet: 0.27 (0.28), residues: 318 loop : -1.02 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 193 TYR 0.039 0.004 TYR B 66 PHE 0.029 0.003 PHE b 399 TRP 0.037 0.004 TRP b 386 HIS 0.010 0.002 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00599 (12231) covalent geometry : angle 0.95765 (16650) SS BOND : bond 0.00707 ( 21) SS BOND : angle 1.58255 ( 42) hydrogen bonds : bond 0.05520 ( 531) hydrogen bonds : angle 5.92765 ( 1458) link_ALPHA1-3 : bond 0.00642 ( 3) link_ALPHA1-3 : angle 4.59923 ( 9) link_ALPHA1-6 : bond 0.01998 ( 3) link_ALPHA1-6 : angle 2.26162 ( 9) link_BETA1-4 : bond 0.00827 ( 42) link_BETA1-4 : angle 2.90220 ( 126) link_BETA1-6 : bond 0.02760 ( 6) link_BETA1-6 : angle 6.54463 ( 18) link_NAG-ASN : bond 0.00461 ( 33) link_NAG-ASN : angle 2.52402 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 223 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7122 (ppp) cc_final: 0.6567 (ppp) REVERT: A 134 MET cc_start: 0.8011 (tmm) cc_final: 0.5776 (mtt) REVERT: A 156 ASP cc_start: 0.7456 (t0) cc_final: 0.7064 (t70) REVERT: A 161 LYS cc_start: 0.8625 (ptpp) cc_final: 0.8240 (pttm) REVERT: A 200 TYR cc_start: 0.8372 (p90) cc_final: 0.8109 (p90) REVERT: A 217 TYR cc_start: 0.7306 (m-80) cc_final: 0.6780 (m-80) REVERT: A 236 PRO cc_start: 0.9052 (Cg_endo) cc_final: 0.8829 (Cg_exo) REVERT: a 331 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: a 351 MET cc_start: 0.8880 (mmp) cc_final: 0.8646 (tpp) REVERT: a 363 TYR cc_start: 0.7640 (p90) cc_final: 0.7343 (p90) REVERT: a 408 ASP cc_start: 0.7630 (t0) cc_final: 0.7321 (t70) REVERT: B 96 MET cc_start: 0.7489 (ppp) cc_final: 0.7108 (ppp) REVERT: B 134 MET cc_start: 0.8080 (tmm) cc_final: 0.5840 (mtt) REVERT: B 193 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.8079 (mtm-85) REVERT: B 200 TYR cc_start: 0.8414 (p90) cc_final: 0.8194 (p90) REVERT: B 217 TYR cc_start: 0.7719 (m-80) cc_final: 0.7402 (m-80) REVERT: B 236 PRO cc_start: 0.9136 (Cg_endo) cc_final: 0.8678 (Cg_exo) REVERT: b 308 GLU cc_start: 0.8077 (pm20) cc_final: 0.7702 (pm20) REVERT: b 408 ASP cc_start: 0.7581 (t0) cc_final: 0.7275 (t70) REVERT: b 410 MET cc_start: 0.9123 (mtt) cc_final: 0.8715 (mtp) REVERT: C 116 LYS cc_start: 0.8035 (mttt) cc_final: 0.7461 (tptt) REVERT: C 156 ASP cc_start: 0.7197 (t0) cc_final: 0.6473 (t70) REVERT: C 161 LYS cc_start: 0.8497 (ptpp) cc_final: 0.7769 (pttt) REVERT: C 193 ARG cc_start: 0.8302 (mtm180) cc_final: 0.8049 (mtm-85) REVERT: C 236 PRO cc_start: 0.8656 (Cg_endo) cc_final: 0.8274 (Cg_exo) REVERT: c 311 ASP cc_start: 0.9058 (m-30) cc_final: 0.8788 (m-30) REVERT: c 363 TYR cc_start: 0.7261 (p90) cc_final: 0.6618 (p90) REVERT: c 408 ASP cc_start: 0.7547 (t0) cc_final: 0.7284 (t70) outliers start: 7 outliers final: 0 residues processed: 226 average time/residue: 0.1042 time to fit residues: 33.6374 Evaluate side-chains 169 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 90 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 103 optimal weight: 40.0000 chunk 51 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 124 optimal weight: 0.0870 chunk 147 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 overall best weight: 3.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 406 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.074045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.062879 restraints weight = 81667.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.064133 restraints weight = 55484.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.065108 restraints weight = 42030.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.065781 restraints weight = 34236.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066178 restraints weight = 29530.123| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12339 Z= 0.230 Angle : 0.963 18.403 16953 Z= 0.445 Chirality : 0.051 0.436 2202 Planarity : 0.004 0.045 2070 Dihedral : 10.965 86.205 3450 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.67 (0.20), residues: 1605 helix: 0.79 (0.29), residues: 324 sheet: 0.17 (0.28), residues: 330 loop : -1.14 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 325 TYR 0.041 0.003 TYR c 366 PHE 0.014 0.002 PHE b 316 TRP 0.025 0.003 TRP a 386 HIS 0.008 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00474 (12231) covalent geometry : angle 0.86797 (16650) SS BOND : bond 0.00456 ( 21) SS BOND : angle 1.18186 ( 42) hydrogen bonds : bond 0.04974 ( 531) hydrogen bonds : angle 5.76161 ( 1458) link_ALPHA1-3 : bond 0.00227 ( 3) link_ALPHA1-3 : angle 4.16318 ( 9) link_ALPHA1-6 : bond 0.01963 ( 3) link_ALPHA1-6 : angle 3.22746 ( 9) link_BETA1-4 : bond 0.00450 ( 42) link_BETA1-4 : angle 2.70717 ( 126) link_BETA1-6 : bond 0.03084 ( 6) link_BETA1-6 : angle 6.43339 ( 18) link_NAG-ASN : bond 0.00447 ( 33) link_NAG-ASN : angle 3.50037 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9179 (mp) cc_final: 0.8654 (mp) REVERT: A 75 MET cc_start: 0.7608 (mmm) cc_final: 0.7082 (mmm) REVERT: A 96 MET cc_start: 0.7289 (ppp) cc_final: 0.6536 (ppp) REVERT: A 134 MET cc_start: 0.7849 (tmm) cc_final: 0.6033 (mtt) REVERT: A 217 TYR cc_start: 0.7200 (m-80) cc_final: 0.6694 (m-80) REVERT: a 311 ASP cc_start: 0.9126 (m-30) cc_final: 0.8828 (m-30) REVERT: a 325 ARG cc_start: 0.8612 (mmt180) cc_final: 0.8217 (mmt-90) REVERT: a 351 MET cc_start: 0.8950 (mmp) cc_final: 0.8712 (tpp) REVERT: a 363 TYR cc_start: 0.7558 (p90) cc_final: 0.7337 (p90) REVERT: a 408 ASP cc_start: 0.7633 (t0) cc_final: 0.7375 (t70) REVERT: B 96 MET cc_start: 0.7747 (ppp) cc_final: 0.7238 (ppp) REVERT: B 134 MET cc_start: 0.7954 (tmm) cc_final: 0.5774 (mtt) REVERT: B 161 LYS cc_start: 0.8538 (pttm) cc_final: 0.8238 (pttt) REVERT: B 193 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.8234 (mtm-85) REVERT: B 194 MET cc_start: 0.8060 (ptp) cc_final: 0.7831 (ptp) REVERT: B 200 TYR cc_start: 0.8381 (p90) cc_final: 0.8072 (p90) REVERT: B 217 TYR cc_start: 0.7774 (m-80) cc_final: 0.7431 (m-80) REVERT: b 308 GLU cc_start: 0.8012 (pm20) cc_final: 0.7776 (mp0) REVERT: b 325 ARG cc_start: 0.8879 (mmt-90) cc_final: 0.8672 (mmt180) REVERT: b 333 SER cc_start: 0.9075 (p) cc_final: 0.8769 (m) REVERT: b 408 ASP cc_start: 0.7524 (t0) cc_final: 0.7205 (t70) REVERT: C 72 GLU cc_start: 0.8464 (mp0) cc_final: 0.8196 (mp0) REVERT: C 75 MET cc_start: 0.7625 (mmm) cc_final: 0.7316 (mmm) REVERT: C 96 MET cc_start: 0.7948 (ppp) cc_final: 0.7170 (ppp) REVERT: C 116 LYS cc_start: 0.8035 (mttt) cc_final: 0.7503 (tptt) REVERT: C 236 PRO cc_start: 0.8971 (Cg_endo) cc_final: 0.8400 (Cg_exo) REVERT: c 311 ASP cc_start: 0.9071 (m-30) cc_final: 0.8727 (m-30) REVERT: c 333 SER cc_start: 0.9288 (p) cc_final: 0.9039 (m) REVERT: c 363 TYR cc_start: 0.7250 (p90) cc_final: 0.6944 (p90) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1108 time to fit residues: 36.3638 Evaluate side-chains 169 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 99 optimal weight: 40.0000 chunk 76 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 130 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 104 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS C 218 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.070946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059939 restraints weight = 83471.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061187 restraints weight = 55772.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.062065 restraints weight = 41869.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.062605 restraints weight = 34143.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.063054 restraints weight = 29998.287| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 12339 Z= 0.310 Angle : 1.057 18.331 16953 Z= 0.493 Chirality : 0.050 0.348 2202 Planarity : 0.005 0.058 2070 Dihedral : 10.705 77.686 3450 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.12 % Allowed : 6.43 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1605 helix: -0.23 (0.27), residues: 324 sheet: -0.13 (0.28), residues: 342 loop : -1.60 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 193 TYR 0.026 0.004 TYR c 366 PHE 0.029 0.003 PHE C 157 TRP 0.032 0.003 TRP C 210 HIS 0.015 0.002 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00643 (12231) covalent geometry : angle 0.95615 (16650) SS BOND : bond 0.00942 ( 21) SS BOND : angle 1.50626 ( 42) hydrogen bonds : bond 0.05420 ( 531) hydrogen bonds : angle 6.26048 ( 1458) link_ALPHA1-3 : bond 0.00121 ( 3) link_ALPHA1-3 : angle 4.25591 ( 9) link_ALPHA1-6 : bond 0.01954 ( 3) link_ALPHA1-6 : angle 4.44477 ( 9) link_BETA1-4 : bond 0.00663 ( 42) link_BETA1-4 : angle 2.70955 ( 126) link_BETA1-6 : bond 0.03316 ( 6) link_BETA1-6 : angle 6.67501 ( 18) link_NAG-ASN : bond 0.00494 ( 33) link_NAG-ASN : angle 3.97888 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7781 (ppp) cc_final: 0.7114 (ppp) REVERT: A 134 MET cc_start: 0.7691 (tmm) cc_final: 0.6028 (mtt) REVERT: A 200 TYR cc_start: 0.8374 (p90) cc_final: 0.8107 (p90) REVERT: A 217 TYR cc_start: 0.7521 (m-80) cc_final: 0.6951 (m-80) REVERT: a 308 GLU cc_start: 0.8571 (mp0) cc_final: 0.7860 (mp0) REVERT: a 351 MET cc_start: 0.9062 (mmp) cc_final: 0.8740 (tpp) REVERT: a 363 TYR cc_start: 0.7733 (p90) cc_final: 0.7365 (p90) REVERT: B 75 MET cc_start: 0.7606 (mtt) cc_final: 0.7330 (mtt) REVERT: B 96 MET cc_start: 0.7876 (ppp) cc_final: 0.7238 (ppp) REVERT: B 134 MET cc_start: 0.7673 (tmm) cc_final: 0.6080 (mtt) REVERT: B 217 TYR cc_start: 0.7938 (m-80) cc_final: 0.7543 (m-80) REVERT: b 308 GLU cc_start: 0.8236 (pm20) cc_final: 0.7878 (mp0) REVERT: b 311 ASP cc_start: 0.9120 (m-30) cc_final: 0.8757 (m-30) REVERT: b 372 LEU cc_start: 0.7295 (tp) cc_final: 0.6164 (tp) REVERT: b 410 MET cc_start: 0.9369 (mtp) cc_final: 0.9079 (mtp) REVERT: C 96 MET cc_start: 0.8295 (ppp) cc_final: 0.7531 (ppp) REVERT: C 116 LYS cc_start: 0.8088 (mttt) cc_final: 0.7440 (tptt) REVERT: C 134 MET cc_start: 0.7967 (tmm) cc_final: 0.7256 (ttt) REVERT: C 193 ARG cc_start: 0.8686 (mtm180) cc_final: 0.8294 (mtp85) REVERT: C 236 PRO cc_start: 0.8761 (Cg_endo) cc_final: 0.8335 (Cg_exo) REVERT: c 284 MET cc_start: 0.8315 (ptp) cc_final: 0.7997 (ptp) REVERT: c 311 ASP cc_start: 0.9177 (m-30) cc_final: 0.8941 (m-30) REVERT: c 410 MET cc_start: 0.8977 (mtt) cc_final: 0.8627 (mtp) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.1055 time to fit residues: 31.2457 Evaluate side-chains 159 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 118 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS a 338 ASN c 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.073728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.062453 restraints weight = 80693.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063761 restraints weight = 53622.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064681 restraints weight = 40163.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.065314 restraints weight = 32694.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.065704 restraints weight = 28369.465| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12339 Z= 0.180 Angle : 0.916 17.182 16953 Z= 0.420 Chirality : 0.049 0.342 2202 Planarity : 0.004 0.052 2070 Dihedral : 10.137 69.773 3450 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.20), residues: 1605 helix: 0.10 (0.28), residues: 327 sheet: -0.26 (0.27), residues: 342 loop : -1.49 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 193 TYR 0.028 0.002 TYR c 371 PHE 0.021 0.002 PHE C 191 TRP 0.016 0.002 TRP C 210 HIS 0.016 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00374 (12231) covalent geometry : angle 0.81369 (16650) SS BOND : bond 0.00375 ( 21) SS BOND : angle 1.16886 ( 42) hydrogen bonds : bond 0.04537 ( 531) hydrogen bonds : angle 5.87105 ( 1458) link_ALPHA1-3 : bond 0.00119 ( 3) link_ALPHA1-3 : angle 4.26876 ( 9) link_ALPHA1-6 : bond 0.01934 ( 3) link_ALPHA1-6 : angle 3.99194 ( 9) link_BETA1-4 : bond 0.00503 ( 42) link_BETA1-4 : angle 2.41617 ( 126) link_BETA1-6 : bond 0.03053 ( 6) link_BETA1-6 : angle 6.36497 ( 18) link_NAG-ASN : bond 0.00337 ( 33) link_NAG-ASN : angle 3.73454 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7600 (ppp) cc_final: 0.6961 (ppp) REVERT: A 134 MET cc_start: 0.7597 (tmm) cc_final: 0.6084 (mtt) REVERT: A 217 TYR cc_start: 0.7339 (m-80) cc_final: 0.6752 (m-80) REVERT: A 227 TRP cc_start: 0.7307 (p90) cc_final: 0.6931 (p90) REVERT: a 308 GLU cc_start: 0.8443 (mp0) cc_final: 0.8219 (pm20) REVERT: a 325 ARG cc_start: 0.8593 (mmt180) cc_final: 0.8224 (mmt-90) REVERT: a 334 ILE cc_start: 0.8159 (mp) cc_final: 0.7922 (mp) REVERT: a 410 MET cc_start: 0.9078 (mtt) cc_final: 0.8837 (mtp) REVERT: B 82 MET cc_start: 0.8854 (ptp) cc_final: 0.7960 (pmm) REVERT: B 96 MET cc_start: 0.7651 (ppp) cc_final: 0.7047 (ppp) REVERT: B 134 MET cc_start: 0.7552 (tmm) cc_final: 0.5929 (mtt) REVERT: B 161 LYS cc_start: 0.8298 (pttm) cc_final: 0.8057 (pttp) REVERT: B 217 TYR cc_start: 0.7822 (m-80) cc_final: 0.7327 (m-80) REVERT: b 284 MET cc_start: 0.8088 (ptp) cc_final: 0.7659 (ptp) REVERT: b 308 GLU cc_start: 0.8279 (pm20) cc_final: 0.7753 (mp0) REVERT: b 311 ASP cc_start: 0.9001 (m-30) cc_final: 0.8600 (m-30) REVERT: b 334 ILE cc_start: 0.8851 (mm) cc_final: 0.8604 (mm) REVERT: b 356 ARG cc_start: 0.9035 (mpp80) cc_final: 0.8814 (mpp80) REVERT: b 363 TYR cc_start: 0.7570 (p90) cc_final: 0.7235 (p90) REVERT: b 372 LEU cc_start: 0.6899 (tp) cc_final: 0.5796 (tp) REVERT: b 410 MET cc_start: 0.9354 (mtp) cc_final: 0.8986 (mtp) REVERT: C 75 MET cc_start: 0.7568 (mmm) cc_final: 0.7269 (mmm) REVERT: C 82 MET cc_start: 0.8928 (ptp) cc_final: 0.8300 (pmm) REVERT: C 94 TYR cc_start: 0.7522 (p90) cc_final: 0.6989 (p90) REVERT: C 96 MET cc_start: 0.8171 (ppp) cc_final: 0.7586 (ppp) REVERT: C 116 LYS cc_start: 0.7999 (mttt) cc_final: 0.7338 (tptt) REVERT: C 134 MET cc_start: 0.7774 (tmm) cc_final: 0.7107 (ttt) REVERT: C 142 LEU cc_start: 0.9050 (pp) cc_final: 0.8805 (mm) REVERT: C 236 PRO cc_start: 0.8682 (Cg_endo) cc_final: 0.8382 (Cg_exo) REVERT: c 284 MET cc_start: 0.8230 (ptp) cc_final: 0.7980 (ptp) REVERT: c 311 ASP cc_start: 0.9154 (m-30) cc_final: 0.8851 (m-30) REVERT: c 363 TYR cc_start: 0.7511 (p90) cc_final: 0.6886 (p90) REVERT: c 410 MET cc_start: 0.8997 (mtt) cc_final: 0.8669 (mtp) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1103 time to fit residues: 34.6827 Evaluate side-chains 168 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 99 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 146 optimal weight: 30.0000 chunk 147 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 133 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 146 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.071196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.060092 restraints weight = 82186.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.061308 restraints weight = 54980.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.062169 restraints weight = 41413.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062781 restraints weight = 34053.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.063227 restraints weight = 29520.927| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 12339 Z= 0.275 Angle : 1.013 15.897 16953 Z= 0.474 Chirality : 0.051 0.346 2202 Planarity : 0.005 0.047 2070 Dihedral : 10.357 66.898 3450 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.19), residues: 1605 helix: -0.22 (0.27), residues: 324 sheet: -0.58 (0.25), residues: 357 loop : -1.84 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 193 TYR 0.028 0.003 TYR C 217 PHE 0.019 0.003 PHE C 191 TRP 0.035 0.003 TRP C 227 HIS 0.010 0.002 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00573 (12231) covalent geometry : angle 0.91796 (16650) SS BOND : bond 0.00617 ( 21) SS BOND : angle 1.78297 ( 42) hydrogen bonds : bond 0.05160 ( 531) hydrogen bonds : angle 6.28762 ( 1458) link_ALPHA1-3 : bond 0.00100 ( 3) link_ALPHA1-3 : angle 4.20372 ( 9) link_ALPHA1-6 : bond 0.01579 ( 3) link_ALPHA1-6 : angle 4.57036 ( 9) link_BETA1-4 : bond 0.00564 ( 42) link_BETA1-4 : angle 2.45735 ( 126) link_BETA1-6 : bond 0.03177 ( 6) link_BETA1-6 : angle 6.69364 ( 18) link_NAG-ASN : bond 0.00344 ( 33) link_NAG-ASN : angle 3.67080 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7784 (ppp) cc_final: 0.7127 (ppp) REVERT: A 134 MET cc_start: 0.7730 (tmm) cc_final: 0.7211 (ttt) REVERT: A 217 TYR cc_start: 0.7338 (m-80) cc_final: 0.6763 (m-80) REVERT: a 284 MET cc_start: 0.7369 (pmm) cc_final: 0.7054 (pmm) REVERT: a 308 GLU cc_start: 0.8694 (mp0) cc_final: 0.7860 (mp0) REVERT: a 311 ASP cc_start: 0.9216 (m-30) cc_final: 0.8881 (m-30) REVERT: a 351 MET cc_start: 0.8795 (tpp) cc_final: 0.8265 (tpp) REVERT: a 410 MET cc_start: 0.8998 (mtt) cc_final: 0.8773 (mtp) REVERT: B 96 MET cc_start: 0.7814 (ppp) cc_final: 0.7079 (ppp) REVERT: B 134 MET cc_start: 0.7624 (tmm) cc_final: 0.6175 (mtt) REVERT: B 217 TYR cc_start: 0.7714 (m-80) cc_final: 0.7156 (m-80) REVERT: B 236 PRO cc_start: 0.9049 (Cg_endo) cc_final: 0.8603 (Cg_exo) REVERT: b 284 MET cc_start: 0.8191 (ptp) cc_final: 0.7767 (ptp) REVERT: b 308 GLU cc_start: 0.8429 (pm20) cc_final: 0.7895 (mp0) REVERT: b 311 ASP cc_start: 0.8994 (m-30) cc_final: 0.8566 (m-30) REVERT: b 363 TYR cc_start: 0.7635 (p90) cc_final: 0.7258 (p90) REVERT: C 75 MET cc_start: 0.7986 (mmm) cc_final: 0.7726 (mmm) REVERT: C 82 MET cc_start: 0.9122 (ptp) cc_final: 0.8669 (pmm) REVERT: C 96 MET cc_start: 0.8314 (ppp) cc_final: 0.7593 (ppp) REVERT: C 116 LYS cc_start: 0.7954 (mttt) cc_final: 0.7323 (tptt) REVERT: C 134 MET cc_start: 0.7917 (tmm) cc_final: 0.7220 (ttt) REVERT: C 193 ARG cc_start: 0.8527 (mtm180) cc_final: 0.8101 (mtp85) REVERT: C 236 PRO cc_start: 0.8495 (Cg_endo) cc_final: 0.8125 (Cg_exo) REVERT: c 284 MET cc_start: 0.8308 (ptp) cc_final: 0.7947 (ptp) REVERT: c 311 ASP cc_start: 0.9182 (m-30) cc_final: 0.8793 (m-30) REVERT: c 332 MET cc_start: 0.6957 (mtt) cc_final: 0.6379 (mtt) REVERT: c 410 MET cc_start: 0.9039 (mtt) cc_final: 0.8809 (mtp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1086 time to fit residues: 30.7819 Evaluate side-chains 157 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.072110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.061032 restraints weight = 81036.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.062276 restraints weight = 53872.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.063156 restraints weight = 40502.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063785 restraints weight = 33042.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.064224 restraints weight = 28585.698| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12339 Z= 0.229 Angle : 0.959 14.652 16953 Z= 0.446 Chirality : 0.050 0.380 2202 Planarity : 0.004 0.057 2070 Dihedral : 9.981 62.212 3450 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.19), residues: 1605 helix: -0.16 (0.27), residues: 327 sheet: -0.67 (0.25), residues: 357 loop : -1.89 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 193 TYR 0.034 0.003 TYR c 371 PHE 0.027 0.003 PHE C 157 TRP 0.030 0.003 TRP C 210 HIS 0.008 0.002 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00481 (12231) covalent geometry : angle 0.86951 (16650) SS BOND : bond 0.00892 ( 21) SS BOND : angle 1.58247 ( 42) hydrogen bonds : bond 0.04800 ( 531) hydrogen bonds : angle 6.18026 ( 1458) link_ALPHA1-3 : bond 0.00054 ( 3) link_ALPHA1-3 : angle 4.22297 ( 9) link_ALPHA1-6 : bond 0.01714 ( 3) link_ALPHA1-6 : angle 4.33635 ( 9) link_BETA1-4 : bond 0.00540 ( 42) link_BETA1-4 : angle 2.26487 ( 126) link_BETA1-6 : bond 0.03135 ( 6) link_BETA1-6 : angle 6.57686 ( 18) link_NAG-ASN : bond 0.00288 ( 33) link_NAG-ASN : angle 3.39287 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8037 (mmm) cc_final: 0.7659 (mmm) REVERT: A 96 MET cc_start: 0.7786 (ppp) cc_final: 0.7155 (ppp) REVERT: A 134 MET cc_start: 0.7625 (tmm) cc_final: 0.6100 (mtt) REVERT: A 217 TYR cc_start: 0.7237 (m-80) cc_final: 0.6573 (m-80) REVERT: a 284 MET cc_start: 0.7551 (pmm) cc_final: 0.7209 (pmm) REVERT: a 308 GLU cc_start: 0.8643 (mp0) cc_final: 0.7931 (mp0) REVERT: a 311 ASP cc_start: 0.9204 (m-30) cc_final: 0.8868 (m-30) REVERT: a 410 MET cc_start: 0.9108 (mtt) cc_final: 0.8835 (mtp) REVERT: B 96 MET cc_start: 0.7835 (ppp) cc_final: 0.7137 (ppp) REVERT: B 134 MET cc_start: 0.7603 (tmm) cc_final: 0.6133 (mtt) REVERT: B 161 LYS cc_start: 0.8071 (pttp) cc_final: 0.7845 (pttp) REVERT: B 217 TYR cc_start: 0.7685 (m-80) cc_final: 0.7078 (m-80) REVERT: B 236 PRO cc_start: 0.9106 (Cg_endo) cc_final: 0.8713 (Cg_exo) REVERT: b 284 MET cc_start: 0.8025 (ptp) cc_final: 0.7623 (ptp) REVERT: b 308 GLU cc_start: 0.8376 (pm20) cc_final: 0.8010 (pm20) REVERT: b 311 ASP cc_start: 0.8970 (m-30) cc_final: 0.8514 (m-30) REVERT: b 363 TYR cc_start: 0.7553 (p90) cc_final: 0.7153 (p90) REVERT: b 410 MET cc_start: 0.9301 (mtm) cc_final: 0.8966 (mtp) REVERT: C 75 MET cc_start: 0.7842 (mmm) cc_final: 0.7596 (mmm) REVERT: C 96 MET cc_start: 0.8279 (ppp) cc_final: 0.7549 (ppp) REVERT: C 116 LYS cc_start: 0.7948 (mttt) cc_final: 0.7337 (tptt) REVERT: C 134 MET cc_start: 0.7792 (tmm) cc_final: 0.7174 (ttt) REVERT: C 142 LEU cc_start: 0.9040 (pp) cc_final: 0.8724 (mm) REVERT: C 193 ARG cc_start: 0.8491 (mtm180) cc_final: 0.8281 (mtm180) REVERT: C 200 TYR cc_start: 0.8196 (p90) cc_final: 0.7851 (p90) REVERT: C 236 PRO cc_start: 0.8501 (Cg_endo) cc_final: 0.8169 (Cg_exo) REVERT: c 284 MET cc_start: 0.8250 (ptp) cc_final: 0.7945 (ptp) REVERT: c 311 ASP cc_start: 0.9131 (m-30) cc_final: 0.8830 (m-30) REVERT: c 332 MET cc_start: 0.6521 (mtt) cc_final: 0.5857 (mtt) REVERT: c 410 MET cc_start: 0.9023 (mtt) cc_final: 0.8755 (mtp) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1014 time to fit residues: 30.7893 Evaluate side-chains 162 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 73 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 chunk 13 optimal weight: 0.0470 chunk 147 optimal weight: 6.9990 chunk 32 optimal weight: 40.0000 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN C 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.075430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.064224 restraints weight = 79117.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.065550 restraints weight = 52637.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.066525 restraints weight = 39162.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.067110 restraints weight = 31711.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.067612 restraints weight = 27605.713| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12339 Z= 0.154 Angle : 0.874 13.555 16953 Z= 0.407 Chirality : 0.049 0.347 2202 Planarity : 0.004 0.051 2070 Dihedral : 8.989 58.255 3450 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.20), residues: 1605 helix: 0.27 (0.28), residues: 327 sheet: -0.70 (0.26), residues: 339 loop : -1.53 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 193 TYR 0.022 0.002 TYR b 369 PHE 0.041 0.002 PHE C 233 TRP 0.014 0.002 TRP C 210 HIS 0.010 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00321 (12231) covalent geometry : angle 0.79452 (16650) SS BOND : bond 0.00436 ( 21) SS BOND : angle 1.53354 ( 42) hydrogen bonds : bond 0.03967 ( 531) hydrogen bonds : angle 5.69454 ( 1458) link_ALPHA1-3 : bond 0.00011 ( 3) link_ALPHA1-3 : angle 4.21121 ( 9) link_ALPHA1-6 : bond 0.01737 ( 3) link_ALPHA1-6 : angle 3.73705 ( 9) link_BETA1-4 : bond 0.00565 ( 42) link_BETA1-4 : angle 2.02997 ( 126) link_BETA1-6 : bond 0.03105 ( 6) link_BETA1-6 : angle 6.20737 ( 18) link_NAG-ASN : bond 0.00371 ( 33) link_NAG-ASN : angle 2.92790 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7497 (ppp) cc_final: 0.6834 (ppp) REVERT: A 134 MET cc_start: 0.7418 (tmm) cc_final: 0.6024 (mtt) REVERT: a 284 MET cc_start: 0.7652 (pmm) cc_final: 0.7276 (pmm) REVERT: a 308 GLU cc_start: 0.8431 (mp0) cc_final: 0.7663 (mp0) REVERT: a 311 ASP cc_start: 0.9009 (m-30) cc_final: 0.8751 (m-30) REVERT: a 325 ARG cc_start: 0.8483 (mmt180) cc_final: 0.8230 (mmt-90) REVERT: a 410 MET cc_start: 0.9074 (mtt) cc_final: 0.8820 (mtp) REVERT: B 82 MET cc_start: 0.8819 (ptp) cc_final: 0.8248 (pmm) REVERT: B 96 MET cc_start: 0.7645 (ppp) cc_final: 0.7098 (ppp) REVERT: B 134 MET cc_start: 0.7546 (tmm) cc_final: 0.6088 (mtt) REVERT: B 217 TYR cc_start: 0.7583 (m-80) cc_final: 0.7036 (m-80) REVERT: B 236 PRO cc_start: 0.9110 (Cg_endo) cc_final: 0.8696 (Cg_exo) REVERT: b 284 MET cc_start: 0.8048 (ptp) cc_final: 0.7649 (ptp) REVERT: b 308 GLU cc_start: 0.7802 (pm20) cc_final: 0.7569 (pm20) REVERT: b 311 ASP cc_start: 0.8837 (m-30) cc_final: 0.8538 (m-30) REVERT: b 325 ARG cc_start: 0.8862 (mmt180) cc_final: 0.8563 (mmt-90) REVERT: b 410 MET cc_start: 0.9241 (mtm) cc_final: 0.8923 (mtp) REVERT: C 75 MET cc_start: 0.7403 (mmm) cc_final: 0.7132 (mmm) REVERT: C 96 MET cc_start: 0.8102 (ppp) cc_final: 0.7394 (ppp) REVERT: C 116 LYS cc_start: 0.7941 (mttt) cc_final: 0.7242 (tptt) REVERT: C 142 LEU cc_start: 0.8913 (pp) cc_final: 0.8634 (mm) REVERT: C 200 TYR cc_start: 0.8108 (p90) cc_final: 0.7850 (p90) REVERT: c 284 MET cc_start: 0.8279 (ptp) cc_final: 0.7933 (ptp) REVERT: c 311 ASP cc_start: 0.9073 (m-30) cc_final: 0.8786 (m-30) REVERT: c 332 MET cc_start: 0.6266 (mtt) cc_final: 0.5774 (mtt) REVERT: c 410 MET cc_start: 0.8965 (mtt) cc_final: 0.8739 (mtp) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.0997 time to fit residues: 31.4071 Evaluate side-chains 170 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 95 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 150 optimal weight: 50.0000 chunk 82 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.073140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.061764 restraints weight = 78412.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.063097 restraints weight = 51463.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.064013 restraints weight = 38040.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064603 restraints weight = 30841.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.065109 restraints weight = 26759.007| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.7041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12339 Z= 0.205 Angle : 0.923 13.044 16953 Z= 0.434 Chirality : 0.049 0.335 2202 Planarity : 0.005 0.061 2070 Dihedral : 8.961 57.407 3450 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.19), residues: 1605 helix: -0.05 (0.28), residues: 330 sheet: -0.70 (0.25), residues: 351 loop : -1.69 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 193 TYR 0.034 0.003 TYR c 371 PHE 0.028 0.003 PHE A 233 TRP 0.032 0.003 TRP A 210 HIS 0.006 0.002 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00435 (12231) covalent geometry : angle 0.83971 (16650) SS BOND : bond 0.00395 ( 21) SS BOND : angle 1.41040 ( 42) hydrogen bonds : bond 0.04491 ( 531) hydrogen bonds : angle 5.91455 ( 1458) link_ALPHA1-3 : bond 0.00068 ( 3) link_ALPHA1-3 : angle 4.11217 ( 9) link_ALPHA1-6 : bond 0.01430 ( 3) link_ALPHA1-6 : angle 4.44453 ( 9) link_BETA1-4 : bond 0.00514 ( 42) link_BETA1-4 : angle 2.14239 ( 126) link_BETA1-6 : bond 0.02975 ( 6) link_BETA1-6 : angle 6.51011 ( 18) link_NAG-ASN : bond 0.00268 ( 33) link_NAG-ASN : angle 3.09761 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7638 (ppp) cc_final: 0.7028 (ppp) REVERT: A 134 MET cc_start: 0.7414 (tmm) cc_final: 0.5953 (mtt) REVERT: a 284 MET cc_start: 0.7630 (pmm) cc_final: 0.7219 (pmm) REVERT: a 308 GLU cc_start: 0.8464 (mp0) cc_final: 0.7739 (mp0) REVERT: a 311 ASP cc_start: 0.9136 (m-30) cc_final: 0.8795 (m-30) REVERT: a 410 MET cc_start: 0.9146 (mtt) cc_final: 0.8870 (mtp) REVERT: B 82 MET cc_start: 0.8915 (ptp) cc_final: 0.8207 (pmm) REVERT: B 96 MET cc_start: 0.7613 (ppp) cc_final: 0.6982 (ppp) REVERT: B 134 MET cc_start: 0.7382 (tmm) cc_final: 0.6003 (mtt) REVERT: B 217 TYR cc_start: 0.7789 (m-80) cc_final: 0.7211 (m-80) REVERT: B 236 PRO cc_start: 0.9097 (Cg_endo) cc_final: 0.8562 (Cg_exo) REVERT: b 284 MET cc_start: 0.7991 (ptp) cc_final: 0.7493 (ptp) REVERT: b 311 ASP cc_start: 0.8888 (m-30) cc_final: 0.8467 (m-30) REVERT: b 339 LYS cc_start: 0.9377 (mptt) cc_final: 0.9025 (mppt) REVERT: b 363 TYR cc_start: 0.7267 (p90) cc_final: 0.6879 (p90) REVERT: b 410 MET cc_start: 0.9283 (mtm) cc_final: 0.8965 (mtp) REVERT: C 75 MET cc_start: 0.7810 (mmm) cc_final: 0.7493 (mmm) REVERT: C 96 MET cc_start: 0.8094 (ppp) cc_final: 0.7341 (ppp) REVERT: C 116 LYS cc_start: 0.7953 (mttt) cc_final: 0.7255 (tptt) REVERT: C 142 LEU cc_start: 0.9027 (pp) cc_final: 0.8737 (mm) REVERT: C 200 TYR cc_start: 0.8233 (p90) cc_final: 0.7881 (p90) REVERT: c 284 MET cc_start: 0.8286 (ptp) cc_final: 0.7937 (ptp) REVERT: c 311 ASP cc_start: 0.9129 (m-30) cc_final: 0.8808 (m-30) REVERT: c 332 MET cc_start: 0.6593 (mtt) cc_final: 0.5989 (mtt) REVERT: c 410 MET cc_start: 0.9002 (mtt) cc_final: 0.8737 (mtp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1040 time to fit residues: 31.4139 Evaluate side-chains 163 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 90 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 154 optimal weight: 30.0000 chunk 148 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 406 GLN B 146 ASN C 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.075700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.064390 restraints weight = 79559.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.065729 restraints weight = 52845.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066689 restraints weight = 39208.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.067355 restraints weight = 31676.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.067817 restraints weight = 27266.713| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12339 Z= 0.150 Angle : 0.872 12.487 16953 Z= 0.409 Chirality : 0.048 0.350 2202 Planarity : 0.004 0.049 2070 Dihedral : 8.516 56.467 3450 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.20), residues: 1605 helix: 0.13 (0.28), residues: 330 sheet: -0.57 (0.27), residues: 339 loop : -1.48 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 193 TYR 0.034 0.002 TYR C 94 PHE 0.030 0.002 PHE C 233 TRP 0.035 0.002 TRP B 210 HIS 0.013 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00320 (12231) covalent geometry : angle 0.79549 (16650) SS BOND : bond 0.00384 ( 21) SS BOND : angle 1.42254 ( 42) hydrogen bonds : bond 0.03955 ( 531) hydrogen bonds : angle 5.57018 ( 1458) link_ALPHA1-3 : bond 0.00016 ( 3) link_ALPHA1-3 : angle 4.08283 ( 9) link_ALPHA1-6 : bond 0.01445 ( 3) link_ALPHA1-6 : angle 4.24751 ( 9) link_BETA1-4 : bond 0.00528 ( 42) link_BETA1-4 : angle 1.91968 ( 126) link_BETA1-6 : bond 0.02947 ( 6) link_BETA1-6 : angle 6.26706 ( 18) link_NAG-ASN : bond 0.00296 ( 33) link_NAG-ASN : angle 2.82709 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1864.26 seconds wall clock time: 33 minutes 16.28 seconds (1996.28 seconds total)