Starting phenix.real_space_refine on Fri Jul 3 05:42:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sgf_25109/07_2026/7sgf_25109.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgf_25109/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7sgf_25109/07_2026/7sgf_25109.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sgf_25109/07_2026/7sgf_25109.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sgf_25109/07_2026/7sgf_25109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgf_25109/07_2026/7sgf_25109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sgf_25109/07_2026/7sgf_25109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgf_25109/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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 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 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 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 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 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 chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.94, per 1000 atoms: 0.24 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: 1.42 Conformation dependent library (CDL) restraints added in 746.2 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: 0.33 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: 2.02 Time building geometry restraints manager: 1.75 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 - 17.12: 6306 17.12 - 34.25: 201 34.25 - 51.37: 39 51.37 - 68.50: 9 68.50 - 85.62: 3 Dihedral angle restraints: 6558 sinusoidal: 1878 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 6555 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.690 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 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 : 9.259 68.423 3483 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/Z covalent geometry : bond 0.02183 / 1.20 (12231) covalent geometry : angle 2.04419 / 1.32 (16650) SS BOND : bond 0.01984 / 1.40 ( 21) SS BOND : angle 3.06152 / 1.80 ( 42) hydrogen bonds : bond 0.16954 / 10.93 ( 531) hydrogen bonds : angle 8.18612 / 5.87 ( 1458) link_ALPHA1-3 : bond 0.08879 / 4.45 ( 3) link_ALPHA1-3 : angle 7.95870 / 3.74 ( 9) link_ALPHA1-6 : bond 0.06533 / 3.28 ( 3) link_ALPHA1-6 : angle 2.34277 / 1.12 ( 9) link_BETA1-4 : bond 0.06311 / 3.81 ( 42) link_BETA1-4 : angle 5.06774 / 3.42 ( 126) link_BETA1-6 : bond 0.06288 / 3.70 ( 6) link_BETA1-6 : angle 7.27622 / 4.77 ( 18) link_NAG-ASN : bond 0.07030 / 4.43 ( 33) link_NAG-ASN : angle 3.35269 / 2.09 ( 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 : 0.398 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: 0.1019 time to fit residues: 51.0298 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 : 0.303 ------------------------------------------------------------------------------- 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... A 92 HIS A 141 HIS A 218 GLN a 331 GLN B 92 HIS B 141 HIS B 218 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.076414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.064707 restraints weight = 78268.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066180 restraints weight = 52348.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.067205 restraints weight = 38793.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.067888 restraints weight = 31250.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.068427 restraints weight = 26910.354| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12339 Z= 0.249 Angle : 1.012 12.356 16953 Z= 0.493 Chirality : 0.051 0.320 2202 Planarity : 0.004 0.032 2070 Dihedral : 6.193 31.320 1689 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.47 % Allowed : 5.15 % 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: -0.13 (0.20), residues: 1605 helix: 0.62 (0.27), residues: 345 sheet: 0.75 (0.29), residues: 318 loop : -0.65 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 325 TYR 0.029 0.004 TYR B 66 PHE 0.027 0.002 PHE A 233 TRP 0.013 0.002 TRP c 370 HIS 0.013 0.002 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.24 (12231) covalent geometry : angle 0.93787 / 0.48 (16650) SS BOND : bond 0.00481 / 0.30 ( 21) SS BOND : angle 1.44731 / 0.79 ( 42) hydrogen bonds : bond 0.06042 / 4.08 ( 531) hydrogen bonds : angle 6.15838 / 4.36 ( 1458) link_ALPHA1-3 : bond 0.00882 / 0.44 ( 3) link_ALPHA1-3 : angle 3.79180 / 1.84 ( 9) link_ALPHA1-6 : bond 0.01373 / 0.69 ( 3) link_ALPHA1-6 : angle 1.21367 / 0.71 ( 9) link_BETA1-4 : bond 0.00763 / 0.48 ( 42) link_BETA1-4 : angle 2.96683 / 2.06 ( 126) link_BETA1-6 : bond 0.03487 / 2.05 ( 6) link_BETA1-6 : angle 6.10757 / 4.02 ( 18) link_NAG-ASN : bond 0.00899 / 0.58 ( 33) link_NAG-ASN : angle 2.69061 / 1.68 ( 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 257 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 253 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.8931 (tt) cc_final: 0.8592 (mp) REVERT: A 72 GLU cc_start: 0.8313 (mp0) cc_final: 0.8096 (mp0) REVERT: A 189 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8693 (tp-100) REVERT: A 200 TYR cc_start: 0.8262 (p90) cc_final: 0.7962 (p90) REVERT: A 205 SER cc_start: 0.8493 (p) cc_final: 0.8277 (t) REVERT: A 217 TYR cc_start: 0.7297 (m-80) cc_final: 0.7042 (m-80) REVERT: A 228 GLU cc_start: 0.8463 (pm20) cc_final: 0.7765 (pp20) REVERT: A 236 PRO cc_start: 0.8897 (Cg_endo) cc_final: 0.8280 (Cg_exo) REVERT: a 363 TYR cc_start: 0.7415 (p90) cc_final: 0.7115 (p90) REVERT: a 371 TYR cc_start: 0.6620 (m-80) cc_final: 0.6359 (m-80) REVERT: a 396 GLU cc_start: 0.8650 (mp0) cc_final: 0.8309 (mp0) REVERT: a 408 ASP cc_start: 0.7709 (t0) cc_final: 0.7449 (t70) REVERT: B 100 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8351 (mm-30) REVERT: B 161 LYS cc_start: 0.8484 (ptpp) cc_final: 0.8107 (pttt) REVERT: B 189 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8630 (tp40) REVERT: B 200 TYR cc_start: 0.8286 (p90) cc_final: 0.8047 (p90) REVERT: B 217 TYR cc_start: 0.7360 (m-80) cc_final: 0.7112 (m-80) REVERT: B 228 GLU cc_start: 0.8264 (pm20) cc_final: 0.7890 (pp20) REVERT: B 236 PRO cc_start: 0.9143 (Cg_endo) cc_final: 0.8441 (Cg_exo) REVERT: b 334 ILE cc_start: 0.8383 (mm) cc_final: 0.8168 (mm) REVERT: b 335 GLN cc_start: 0.8930 (pm20) cc_final: 0.8687 (pm20) REVERT: b 396 GLU cc_start: 0.8617 (mp0) cc_final: 0.8183 (mp0) REVERT: b 410 MET cc_start: 0.9270 (mtt) cc_final: 0.9015 (mtp) REVERT: C 100 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8145 (mm-30) REVERT: C 116 LYS cc_start: 0.8061 (mttt) cc_final: 0.7472 (tptt) REVERT: C 134 MET cc_start: 0.7125 (ttp) cc_final: 0.5380 (mtt) REVERT: C 156 ASP cc_start: 0.6874 (t0) cc_final: 0.6268 (t70) REVERT: C 161 LYS cc_start: 0.8593 (ptpp) cc_final: 0.8244 (pttt) REVERT: C 236 PRO cc_start: 0.8936 (Cg_endo) cc_final: 0.8267 (Cg_exo) REVERT: c 316 PHE cc_start: 0.8635 (m-80) cc_final: 0.8399 (m-80) REVERT: c 363 TYR cc_start: 0.7298 (p90) cc_final: 0.7011 (p90) REVERT: c 371 TYR cc_start: 0.7027 (m-80) cc_final: 0.6791 (m-80) REVERT: c 396 GLU cc_start: 0.8676 (mp0) cc_final: 0.8465 (mp0) REVERT: c 410 MET cc_start: 0.9037 (mtt) cc_final: 0.8726 (mtp) outliers start: 4 outliers final: 1 residues processed: 255 average time/residue: 0.0914 time to fit residues: 33.8430 Evaluate side-chains 182 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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: 10.0000 chunk 59 optimal weight: 6.9990 chunk 99 optimal weight: 40.0000 chunk 56 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 150 optimal weight: 30.0000 chunk 25 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS B 230 HIS b 338 ASN b 374 HIS ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 374 HIS ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.073450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.062009 restraints weight = 79727.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063323 restraints weight = 53311.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064298 restraints weight = 40102.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.064981 restraints weight = 32406.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.065493 restraints weight = 27816.220| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 12339 Z= 0.278 Angle : 1.003 13.841 16953 Z= 0.485 Chirality : 0.050 0.351 2202 Planarity : 0.005 0.042 2070 Dihedral : 6.213 29.205 1689 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.58 % Allowed : 7.37 % Favored : 92.05 % 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: -0.69 (0.20), residues: 1605 helix: 0.48 (0.29), residues: 339 sheet: 0.22 (0.28), residues: 318 loop : -1.07 (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 c 366 PHE 0.027 0.003 PHE b 399 TRP 0.028 0.004 TRP b 386 HIS 0.010 0.002 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.28 (12231) covalent geometry : angle 0.93890 / 0.47 (16650) SS BOND : bond 0.00590 / 0.36 ( 21) SS BOND : angle 1.53354 / 0.86 ( 42) hydrogen bonds : bond 0.05432 / 3.58 ( 531) hydrogen bonds : angle 5.99041 / 4.22 ( 1458) link_ALPHA1-3 : bond 0.00422 / 0.21 ( 3) link_ALPHA1-3 : angle 3.47138 / 1.70 ( 9) link_ALPHA1-6 : bond 0.01383 / 0.69 ( 3) link_ALPHA1-6 : angle 1.36683 / 0.79 ( 9) link_BETA1-4 : bond 0.00703 / 0.42 ( 42) link_BETA1-4 : angle 2.41591 / 1.74 ( 126) link_BETA1-6 : bond 0.02443 / 1.46 ( 6) link_BETA1-6 : angle 6.50922 / 4.30 ( 18) link_NAG-ASN : bond 0.00479 / 0.31 ( 33) link_NAG-ASN : angle 2.56448 / 1.62 ( 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 226 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 221 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: A 71 LEU cc_start: 0.8670 (tt) cc_final: 0.8405 (mp) REVERT: A 72 GLU cc_start: 0.8326 (mp0) cc_final: 0.8020 (mp0) REVERT: A 96 MET cc_start: 0.6963 (ppp) cc_final: 0.6382 (ppp) REVERT: A 134 MET cc_start: 0.8269 (tmm) cc_final: 0.5933 (mtt) REVERT: A 156 ASP cc_start: 0.7413 (t0) cc_final: 0.7064 (t70) REVERT: A 161 LYS cc_start: 0.8685 (ptpp) cc_final: 0.8278 (pttm) REVERT: A 200 TYR cc_start: 0.8389 (p90) cc_final: 0.8103 (p90) REVERT: A 217 TYR cc_start: 0.7348 (m-80) cc_final: 0.6816 (m-80) REVERT: a 308 GLU cc_start: 0.8311 (pm20) cc_final: 0.7860 (mp0) REVERT: a 351 MET cc_start: 0.8888 (mmp) cc_final: 0.8683 (tpp) REVERT: a 363 TYR cc_start: 0.7550 (p90) cc_final: 0.7264 (p90) REVERT: a 408 ASP cc_start: 0.7647 (t0) cc_final: 0.7340 (t70) REVERT: a 410 MET cc_start: 0.9116 (mtt) cc_final: 0.8887 (mtp) REVERT: B 96 MET cc_start: 0.7299 (ppp) cc_final: 0.6908 (ppp) REVERT: B 156 ASP cc_start: 0.7362 (t0) cc_final: 0.7107 (t70) REVERT: B 193 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.8075 (mtm-85) REVERT: B 200 TYR cc_start: 0.8398 (p90) cc_final: 0.8175 (p90) REVERT: B 217 TYR cc_start: 0.7263 (m-80) cc_final: 0.6742 (m-80) REVERT: b 308 GLU cc_start: 0.8108 (pm20) cc_final: 0.7725 (pm20) REVERT: b 371 TYR cc_start: 0.7365 (m-80) cc_final: 0.6764 (m-80) REVERT: b 408 ASP cc_start: 0.7589 (t0) cc_final: 0.7262 (t70) REVERT: C 82 MET cc_start: 0.9217 (ptp) cc_final: 0.8992 (ptp) REVERT: C 116 LYS cc_start: 0.8015 (mttt) cc_final: 0.7450 (tptt) REVERT: C 134 MET cc_start: 0.7260 (ttp) cc_final: 0.5830 (mtt) REVERT: C 156 ASP cc_start: 0.7120 (t0) cc_final: 0.6431 (t70) REVERT: C 161 LYS cc_start: 0.8548 (ptpp) cc_final: 0.7800 (pttt) REVERT: c 311 ASP cc_start: 0.9063 (m-30) cc_final: 0.8815 (m-30) REVERT: c 410 MET cc_start: 0.9192 (mtt) cc_final: 0.8992 (mtp) outliers start: 5 outliers final: 0 residues processed: 223 average time/residue: 0.0948 time to fit residues: 30.2190 Evaluate side-chains 175 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 10.0000 chunk 154 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 124 optimal weight: 0.0020 chunk 147 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 overall best weight: 4.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 331 GLN a 374 HIS b 331 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 331 GLN ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.072407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.061112 restraints weight = 80379.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.062385 restraints weight = 53466.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.063326 restraints weight = 40088.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063834 restraints weight = 32628.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064306 restraints weight = 28487.134| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.5263 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= 0.284 Angle : 1.025 19.466 16953 Z= 0.476 Chirality : 0.050 0.424 2202 Planarity : 0.005 0.062 2070 Dihedral : 6.327 32.827 1689 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % 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: -0.85 (0.20), residues: 1605 helix: 0.49 (0.29), residues: 324 sheet: 0.01 (0.28), residues: 342 loop : -1.19 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 193 TYR 0.025 0.003 TYR B 66 PHE 0.016 0.003 PHE c 316 TRP 0.016 0.003 TRP a 386 HIS 0.013 0.002 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.28 (12231) covalent geometry : angle 0.93814 / 0.46 (16650) SS BOND : bond 0.00506 / 0.33 ( 21) SS BOND : angle 1.20023 / 0.69 ( 42) hydrogen bonds : bond 0.05334 / 3.54 ( 531) hydrogen bonds : angle 6.04066 / 4.27 ( 1458) link_ALPHA1-3 : bond 0.00419 / 0.21 ( 3) link_ALPHA1-3 : angle 3.36784 / 1.66 ( 9) link_ALPHA1-6 : bond 0.01526 / 0.77 ( 3) link_ALPHA1-6 : angle 1.51564 / 0.88 ( 9) link_BETA1-4 : bond 0.00621 / 0.41 ( 42) link_BETA1-4 : angle 2.46510 / 1.70 ( 126) link_BETA1-6 : bond 0.03004 / 1.78 ( 6) link_BETA1-6 : angle 6.66294 / 4.36 ( 18) link_NAG-ASN : bond 0.00549 / 0.34 ( 33) link_NAG-ASN : angle 3.76979 / 2.75 ( 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 220 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8357 (mp0) cc_final: 0.8039 (mp0) REVERT: A 96 MET cc_start: 0.7410 (ppp) cc_final: 0.6643 (ppp) REVERT: A 134 MET cc_start: 0.7943 (tmm) cc_final: 0.6034 (mtt) REVERT: A 217 TYR cc_start: 0.7300 (m-80) cc_final: 0.6717 (m-80) REVERT: a 311 ASP cc_start: 0.9197 (m-30) cc_final: 0.8903 (m-30) REVERT: a 351 MET cc_start: 0.8976 (mmp) cc_final: 0.8513 (tpp) REVERT: a 363 TYR cc_start: 0.7616 (p90) cc_final: 0.7364 (p90) REVERT: a 408 ASP cc_start: 0.7651 (t0) cc_final: 0.7337 (t70) REVERT: B 96 MET cc_start: 0.7833 (ppp) cc_final: 0.7310 (ppp) REVERT: B 217 TYR cc_start: 0.7482 (m-80) cc_final: 0.6914 (m-80) REVERT: B 229 ASP cc_start: 0.6821 (p0) cc_final: 0.6509 (p0) REVERT: b 371 TYR cc_start: 0.7560 (m-80) cc_final: 0.6904 (m-80) REVERT: b 410 MET cc_start: 0.9221 (mtt) cc_final: 0.8880 (mtp) REVERT: C 72 GLU cc_start: 0.8382 (mp0) cc_final: 0.8118 (mp0) REVERT: C 96 MET cc_start: 0.7955 (ppp) cc_final: 0.7164 (ppp) REVERT: C 116 LYS cc_start: 0.8073 (mttt) cc_final: 0.7480 (tptt) REVERT: C 134 MET cc_start: 0.7394 (ttp) cc_final: 0.6084 (mtt) REVERT: C 193 ARG cc_start: 0.8430 (mtm180) cc_final: 0.8116 (mtm-85) REVERT: c 284 MET cc_start: 0.8403 (ptp) cc_final: 0.8162 (ptp) REVERT: c 311 ASP cc_start: 0.9161 (m-30) cc_final: 0.8834 (m-30) REVERT: c 333 SER cc_start: 0.9332 (p) cc_final: 0.9043 (m) REVERT: c 339 LYS cc_start: 0.9383 (mppt) cc_final: 0.9094 (mptt) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.0900 time to fit residues: 28.4895 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 : 0.421 ------------------------------------------------------------------------------- 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: 1.9990 chunk 144 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 chunk 14 optimal weight: 0.0370 chunk 130 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 338 ASN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 338 ASN c 406 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.072107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.060344 restraints weight = 79504.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.061711 restraints weight = 52644.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.062659 restraints weight = 38978.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.063299 restraints weight = 31641.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063774 restraints weight = 27346.726| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 12339 Z= 0.256 Angle : 0.972 17.968 16953 Z= 0.453 Chirality : 0.048 0.362 2202 Planarity : 0.004 0.059 2070 Dihedral : 6.265 30.380 1689 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % 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: -1.17 (0.20), residues: 1605 helix: 0.15 (0.28), residues: 324 sheet: -0.08 (0.28), residues: 345 loop : -1.43 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 193 TYR 0.024 0.003 TYR a 366 PHE 0.025 0.003 PHE b 399 TRP 0.015 0.002 TRP b 386 HIS 0.016 0.002 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.25 (12231) covalent geometry : angle 0.88620 / 0.43 (16650) SS BOND : bond 0.00392 / 0.24 ( 21) SS BOND : angle 1.62909 / 1.01 ( 42) hydrogen bonds : bond 0.05082 / 3.36 ( 531) hydrogen bonds : angle 6.09752 / 4.30 ( 1458) link_ALPHA1-3 : bond 0.00277 / 0.14 ( 3) link_ALPHA1-3 : angle 3.41686 / 1.69 ( 9) link_ALPHA1-6 : bond 0.01467 / 0.74 ( 3) link_ALPHA1-6 : angle 1.69040 / 0.97 ( 9) link_BETA1-4 : bond 0.00657 / 0.42 ( 42) link_BETA1-4 : angle 2.17493 / 1.57 ( 126) link_BETA1-6 : bond 0.03317 / 1.99 ( 6) link_BETA1-6 : angle 6.59957 / 4.32 ( 18) link_NAG-ASN : bond 0.00501 / 0.31 ( 33) link_NAG-ASN : angle 3.65904 / 2.69 ( 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 211 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7788 (mmm) cc_final: 0.7553 (mmm) REVERT: A 96 MET cc_start: 0.7721 (ppp) cc_final: 0.7126 (ppp) REVERT: A 134 MET cc_start: 0.7860 (tmm) cc_final: 0.6052 (mtt) REVERT: A 200 TYR cc_start: 0.8324 (p90) cc_final: 0.8108 (p90) REVERT: A 217 TYR cc_start: 0.7493 (m-80) cc_final: 0.6809 (m-80) REVERT: a 308 GLU cc_start: 0.8528 (mp0) cc_final: 0.7892 (mp0) REVERT: a 311 ASP cc_start: 0.9160 (m-30) cc_final: 0.8945 (m-30) REVERT: a 408 ASP cc_start: 0.7624 (t0) cc_final: 0.7273 (t70) REVERT: a 410 MET cc_start: 0.9119 (mtt) cc_final: 0.8862 (mtp) REVERT: B 96 MET cc_start: 0.7813 (ppp) cc_final: 0.7176 (ppp) REVERT: B 200 TYR cc_start: 0.8458 (p90) cc_final: 0.8158 (p90) REVERT: B 217 TYR cc_start: 0.7541 (m-80) cc_final: 0.6869 (m-80) REVERT: b 311 ASP cc_start: 0.9080 (m-30) cc_final: 0.8851 (m-30) REVERT: b 333 SER cc_start: 0.9285 (p) cc_final: 0.8827 (m) REVERT: b 334 ILE cc_start: 0.8857 (mm) cc_final: 0.8633 (mm) REVERT: b 363 TYR cc_start: 0.7419 (p90) cc_final: 0.7158 (p90) REVERT: b 371 TYR cc_start: 0.7500 (m-80) cc_final: 0.7085 (m-80) REVERT: b 410 MET cc_start: 0.9181 (mtt) cc_final: 0.8886 (mtp) REVERT: C 96 MET cc_start: 0.8064 (ppp) cc_final: 0.7504 (ppp) REVERT: C 116 LYS cc_start: 0.8086 (mttt) cc_final: 0.7422 (tptt) REVERT: C 125 LYS cc_start: 0.5523 (mmtt) cc_final: 0.5166 (mmmt) REVERT: C 134 MET cc_start: 0.7376 (ttp) cc_final: 0.5904 (mtt) REVERT: c 284 MET cc_start: 0.8414 (ptp) cc_final: 0.8169 (ptp) REVERT: c 311 ASP cc_start: 0.9207 (m-30) cc_final: 0.8866 (m-30) REVERT: c 410 MET cc_start: 0.9009 (mtt) cc_final: 0.8734 (mtp) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.0946 time to fit residues: 28.5354 Evaluate side-chains 165 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 0.5980 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 338 ASN a 406 GLN b 338 ASN C 189 GLN c 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.073029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.061795 restraints weight = 81854.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.063053 restraints weight = 54699.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.063963 restraints weight = 41217.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064530 restraints weight = 33551.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.065019 restraints weight = 29336.295| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12339 Z= 0.213 Angle : 0.946 17.773 16953 Z= 0.435 Chirality : 0.049 0.362 2202 Planarity : 0.004 0.053 2070 Dihedral : 6.080 29.216 1689 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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: -1.27 (0.20), residues: 1605 helix: 0.19 (0.27), residues: 324 sheet: -0.18 (0.27), residues: 342 loop : -1.52 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 193 TYR 0.022 0.002 TYR c 366 PHE 0.021 0.002 PHE C 157 TRP 0.026 0.002 TRP C 227 HIS 0.007 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (12231) covalent geometry : angle 0.85705 / 0.42 (16650) SS BOND : bond 0.00382 / 0.23 ( 21) SS BOND : angle 1.18713 / 0.71 ( 42) hydrogen bonds : bond 0.04685 / 3.11 ( 531) hydrogen bonds : angle 6.00959 / 4.25 ( 1458) link_ALPHA1-3 : bond 0.00363 / 0.18 ( 3) link_ALPHA1-3 : angle 3.33797 / 1.65 ( 9) link_ALPHA1-6 : bond 0.01594 / 0.80 ( 3) link_ALPHA1-6 : angle 1.73444 / 1.00 ( 9) link_BETA1-4 : bond 0.00638 / 0.40 ( 42) link_BETA1-4 : angle 2.15021 / 1.53 ( 126) link_BETA1-6 : bond 0.03039 / 1.80 ( 6) link_BETA1-6 : angle 6.55655 / 4.32 ( 18) link_NAG-ASN : bond 0.00439 / 0.26 ( 33) link_NAG-ASN : angle 3.73851 / 2.75 ( 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 211 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7724 (mmm) cc_final: 0.7515 (mmm) REVERT: A 96 MET cc_start: 0.7904 (ppp) cc_final: 0.7401 (ppp) REVERT: A 134 MET cc_start: 0.7767 (tmm) cc_final: 0.6002 (mtt) REVERT: A 217 TYR cc_start: 0.7529 (m-80) cc_final: 0.6844 (m-80) REVERT: a 308 GLU cc_start: 0.8437 (mp0) cc_final: 0.8178 (pm20) REVERT: a 311 ASP cc_start: 0.9209 (m-30) cc_final: 0.8914 (m-30) REVERT: a 335 GLN cc_start: 0.9068 (pm20) cc_final: 0.8680 (pm20) REVERT: a 351 MET cc_start: 0.8632 (tpp) cc_final: 0.8272 (tpp) REVERT: a 363 TYR cc_start: 0.7529 (p90) cc_final: 0.7233 (p90) REVERT: a 408 ASP cc_start: 0.7696 (t0) cc_final: 0.7353 (t70) REVERT: a 410 MET cc_start: 0.9149 (mtt) cc_final: 0.8866 (mtp) REVERT: B 75 MET cc_start: 0.7898 (mtt) cc_final: 0.7297 (mmm) REVERT: B 96 MET cc_start: 0.7857 (ppp) cc_final: 0.7243 (ppp) REVERT: B 193 ARG cc_start: 0.8506 (mtm-85) cc_final: 0.8163 (mtm-85) REVERT: B 200 TYR cc_start: 0.8451 (p90) cc_final: 0.8197 (p90) REVERT: B 217 TYR cc_start: 0.7515 (m-80) cc_final: 0.6845 (m-80) REVERT: b 311 ASP cc_start: 0.9053 (m-30) cc_final: 0.8803 (m-30) REVERT: b 332 MET cc_start: 0.7010 (mtt) cc_final: 0.6154 (mtt) REVERT: b 333 SER cc_start: 0.9349 (p) cc_final: 0.9010 (m) REVERT: b 334 ILE cc_start: 0.8938 (mm) cc_final: 0.8686 (mm) REVERT: b 363 TYR cc_start: 0.7377 (p90) cc_final: 0.7069 (p90) REVERT: b 410 MET cc_start: 0.9159 (mtt) cc_final: 0.8876 (mtp) REVERT: C 96 MET cc_start: 0.8199 (ppp) cc_final: 0.7638 (ppp) REVERT: C 116 LYS cc_start: 0.8055 (mttt) cc_final: 0.7383 (tptt) REVERT: C 134 MET cc_start: 0.7311 (ttp) cc_final: 0.5879 (mtt) REVERT: C 193 ARG cc_start: 0.8647 (mtm180) cc_final: 0.8085 (mtm-85) REVERT: C 217 TYR cc_start: 0.7455 (m-10) cc_final: 0.7199 (m-80) REVERT: c 284 MET cc_start: 0.8410 (ptp) cc_final: 0.8109 (ptp) REVERT: c 311 ASP cc_start: 0.9226 (m-30) cc_final: 0.8864 (m-30) REVERT: c 410 MET cc_start: 0.9006 (mtt) cc_final: 0.8767 (mtp) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.0848 time to fit residues: 26.1540 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 : 0.277 ------------------------------------------------------------------------------- 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: 30.0000 chunk 83 optimal weight: 10.0000 chunk 146 optimal weight: 30.0000 chunk 147 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 40.0000 chunk 114 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 338 ASN b 338 ASN C 69 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.070465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059589 restraints weight = 83008.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.060815 restraints weight = 54657.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.061650 restraints weight = 40891.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.062242 restraints weight = 33627.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.062595 restraints weight = 29288.614| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 12339 Z= 0.322 Angle : 1.067 17.548 16953 Z= 0.498 Chirality : 0.052 0.352 2202 Planarity : 0.005 0.049 2070 Dihedral : 6.566 30.430 1689 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % 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: -1.80 (0.19), residues: 1605 helix: -0.33 (0.27), residues: 327 sheet: -0.59 (0.27), residues: 342 loop : -1.81 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 314 TYR 0.039 0.004 TYR b 371 PHE 0.018 0.003 PHE c 316 TRP 0.034 0.003 TRP C 210 HIS 0.009 0.002 HIS C 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.32 (12231) covalent geometry : angle 0.97836 / 0.48 (16650) SS BOND : bond 0.00508 / 0.33 ( 21) SS BOND : angle 1.43443 / 0.94 ( 42) hydrogen bonds : bond 0.05258 / 3.44 ( 531) hydrogen bonds : angle 6.53602 / 4.61 ( 1458) link_ALPHA1-3 : bond 0.00331 / 0.16 ( 3) link_ALPHA1-3 : angle 3.44447 / 1.70 ( 9) link_ALPHA1-6 : bond 0.01575 / 0.79 ( 3) link_ALPHA1-6 : angle 1.85104 / 1.06 ( 9) link_BETA1-4 : bond 0.00640 / 0.40 ( 42) link_BETA1-4 : angle 2.32099 / 1.66 ( 126) link_BETA1-6 : bond 0.03214 / 1.90 ( 6) link_BETA1-6 : angle 6.84120 / 4.49 ( 18) link_NAG-ASN : bond 0.00378 / 0.24 ( 33) link_NAG-ASN : angle 4.03845 / 2.87 ( 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 201 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8073 (mmm) cc_final: 0.7792 (mmm) REVERT: A 96 MET cc_start: 0.8100 (ppp) cc_final: 0.7499 (ppp) REVERT: A 134 MET cc_start: 0.7834 (tmm) cc_final: 0.7293 (ttt) REVERT: a 284 MET cc_start: 0.7820 (ptp) cc_final: 0.7332 (pmm) REVERT: a 308 GLU cc_start: 0.8709 (mp0) cc_final: 0.7961 (mp0) REVERT: a 311 ASP cc_start: 0.9277 (m-30) cc_final: 0.8945 (m-30) REVERT: a 363 TYR cc_start: 0.7563 (p90) cc_final: 0.7168 (p90) REVERT: a 410 MET cc_start: 0.9143 (mtt) cc_final: 0.8821 (mtp) REVERT: B 75 MET cc_start: 0.7936 (mtt) cc_final: 0.7282 (mmm) REVERT: B 96 MET cc_start: 0.7875 (ppp) cc_final: 0.7209 (ppp) REVERT: B 193 ARG cc_start: 0.8466 (mtm-85) cc_final: 0.8114 (mtm-85) REVERT: b 311 ASP cc_start: 0.9114 (m-30) cc_final: 0.8685 (m-30) REVERT: b 332 MET cc_start: 0.7053 (mtt) cc_final: 0.6356 (mtt) REVERT: b 333 SER cc_start: 0.9251 (p) cc_final: 0.8926 (m) REVERT: b 363 TYR cc_start: 0.7521 (p90) cc_final: 0.7189 (p90) REVERT: b 371 TYR cc_start: 0.6839 (m-80) cc_final: 0.6475 (m-80) REVERT: b 410 MET cc_start: 0.9159 (mtt) cc_final: 0.8948 (mtp) REVERT: C 96 MET cc_start: 0.8184 (ppp) cc_final: 0.7508 (ppp) REVERT: C 116 LYS cc_start: 0.7991 (mttt) cc_final: 0.7351 (tptt) REVERT: C 134 MET cc_start: 0.7492 (ttp) cc_final: 0.6142 (mtt) REVERT: C 193 ARG cc_start: 0.8618 (mtm180) cc_final: 0.8184 (mtp85) REVERT: C 217 TYR cc_start: 0.7625 (m-10) cc_final: 0.7384 (m-80) REVERT: c 284 MET cc_start: 0.8315 (ptp) cc_final: 0.8051 (ptp) REVERT: c 311 ASP cc_start: 0.9193 (m-30) cc_final: 0.8879 (m-30) REVERT: c 410 MET cc_start: 0.9100 (mtt) cc_final: 0.8863 (mtp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0859 time to fit residues: 25.3568 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 : 0.374 ------------------------------------------------------------------------------- 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: 0.8980 chunk 85 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 40.0000 chunk 48 optimal weight: 0.4980 chunk 46 optimal weight: 30.0000 chunk 72 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 92 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 338 ASN B 141 HIS B 146 ASN B 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.074652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.063464 restraints weight = 79489.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.064820 restraints weight = 51918.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.065752 restraints weight = 38475.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066384 restraints weight = 31207.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.066759 restraints weight = 27055.363| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.6498 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= 0.162 Angle : 0.914 16.444 16953 Z= 0.421 Chirality : 0.048 0.364 2202 Planarity : 0.004 0.051 2070 Dihedral : 5.879 31.216 1689 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.12 % Allowed : 1.64 % Favored : 98.25 % 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: -1.52 (0.20), residues: 1605 helix: 0.08 (0.28), residues: 327 sheet: -0.61 (0.26), residues: 342 loop : -1.60 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 356 TYR 0.024 0.002 TYR c 371 PHE 0.026 0.002 PHE C 191 TRP 0.019 0.002 TRP A 227 HIS 0.006 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (12231) covalent geometry : angle 0.82939 / 0.40 (16650) SS BOND : bond 0.00388 / 0.26 ( 21) SS BOND : angle 1.76434 / 1.05 ( 42) hydrogen bonds : bond 0.04359 / 2.90 ( 531) hydrogen bonds : angle 6.00056 / 4.27 ( 1458) link_ALPHA1-3 : bond 0.00318 / 0.16 ( 3) link_ALPHA1-3 : angle 3.30470 / 1.64 ( 9) link_ALPHA1-6 : bond 0.01714 / 0.86 ( 3) link_ALPHA1-6 : angle 1.94415 / 1.09 ( 9) link_BETA1-4 : bond 0.00603 / 0.37 ( 42) link_BETA1-4 : angle 2.04706 / 1.46 ( 126) link_BETA1-6 : bond 0.02986 / 1.75 ( 6) link_BETA1-6 : angle 6.35642 / 4.16 ( 18) link_NAG-ASN : bond 0.00391 / 0.28 ( 33) link_NAG-ASN : angle 3.46040 / 2.54 ( 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 226 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7499 (mmm) cc_final: 0.7235 (mmm) REVERT: A 96 MET cc_start: 0.8052 (ppp) cc_final: 0.7559 (ppp) REVERT: A 134 MET cc_start: 0.7677 (tmm) cc_final: 0.7079 (ttt) REVERT: a 308 GLU cc_start: 0.8546 (mp0) cc_final: 0.7835 (mp0) REVERT: a 311 ASP cc_start: 0.9154 (m-30) cc_final: 0.8854 (m-30) REVERT: a 410 MET cc_start: 0.9111 (mtt) cc_final: 0.8796 (mtp) REVERT: B 96 MET cc_start: 0.7964 (ppp) cc_final: 0.7444 (ppp) REVERT: b 311 ASP cc_start: 0.8968 (m-30) cc_final: 0.8602 (m-30) REVERT: b 332 MET cc_start: 0.6774 (mtt) cc_final: 0.6100 (mtt) REVERT: b 410 MET cc_start: 0.9105 (mtt) cc_final: 0.8834 (mtp) REVERT: C 73 LEU cc_start: 0.8820 (mp) cc_final: 0.8570 (mp) REVERT: C 75 MET cc_start: 0.7202 (mtp) cc_final: 0.6738 (ttp) REVERT: C 82 MET cc_start: 0.8951 (ptp) cc_final: 0.8289 (pmm) REVERT: C 96 MET cc_start: 0.8079 (ppp) cc_final: 0.7503 (ppp) REVERT: C 116 LYS cc_start: 0.7965 (mttt) cc_final: 0.7290 (tptt) REVERT: C 134 MET cc_start: 0.7152 (ttp) cc_final: 0.5865 (mtt) REVERT: C 200 TYR cc_start: 0.8100 (p90) cc_final: 0.7894 (p90) REVERT: C 217 TYR cc_start: 0.7549 (m-10) cc_final: 0.7241 (m-80) REVERT: c 284 MET cc_start: 0.8390 (ptp) cc_final: 0.8136 (ptp) REVERT: c 311 ASP cc_start: 0.9099 (m-30) cc_final: 0.8702 (m-30) REVERT: c 363 TYR cc_start: 0.7431 (p90) cc_final: 0.7129 (p90) REVERT: c 410 MET cc_start: 0.9058 (mtt) cc_final: 0.8801 (mtp) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.0859 time to fit residues: 28.6398 Evaluate side-chains 156 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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: 3.9990 chunk 118 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 32 optimal weight: 40.0000 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 338 ASN B 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.073394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.062163 restraints weight = 79089.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.063467 restraints weight = 52294.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.064405 restraints weight = 38822.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.065050 restraints weight = 31419.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.065394 restraints weight = 27078.807| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.6654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12339 Z= 0.190 Angle : 0.919 15.548 16953 Z= 0.430 Chirality : 0.049 0.351 2202 Planarity : 0.004 0.059 2070 Dihedral : 5.825 30.236 1689 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.20), residues: 1605 helix: 0.03 (0.28), residues: 327 sheet: -0.59 (0.25), residues: 357 loop : -1.71 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 193 TYR 0.018 0.002 TYR a 363 PHE 0.024 0.002 PHE A 191 TRP 0.025 0.002 TRP C 210 HIS 0.007 0.001 HIS b 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (12231) covalent geometry : angle 0.83942 / 0.41 (16650) SS BOND : bond 0.00395 / 0.27 ( 21) SS BOND : angle 1.61634 / 0.94 ( 42) hydrogen bonds : bond 0.04345 / 2.85 ( 531) hydrogen bonds : angle 5.95228 / 4.20 ( 1458) link_ALPHA1-3 : bond 0.00339 / 0.17 ( 3) link_ALPHA1-3 : angle 3.12677 / 1.56 ( 9) link_ALPHA1-6 : bond 0.01600 / 0.80 ( 3) link_ALPHA1-6 : angle 1.94148 / 1.09 ( 9) link_BETA1-4 : bond 0.00577 / 0.36 ( 42) link_BETA1-4 : angle 2.02300 / 1.46 ( 126) link_BETA1-6 : bond 0.03108 / 1.84 ( 6) link_BETA1-6 : angle 6.49508 / 4.26 ( 18) link_NAG-ASN : bond 0.00289 / 0.21 ( 33) link_NAG-ASN : angle 3.32113 / 2.46 ( 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 208 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7592 (mmm) cc_final: 0.7368 (mmm) REVERT: A 96 MET cc_start: 0.8183 (ppp) cc_final: 0.7794 (ppp) REVERT: A 134 MET cc_start: 0.7695 (tmm) cc_final: 0.7081 (ttt) REVERT: a 284 MET cc_start: 0.7617 (pmm) cc_final: 0.7234 (pmm) REVERT: a 308 GLU cc_start: 0.8546 (mp0) cc_final: 0.7875 (mp0) REVERT: a 311 ASP cc_start: 0.9136 (m-30) cc_final: 0.8862 (m-30) REVERT: a 410 MET cc_start: 0.9064 (mtt) cc_final: 0.8754 (mtp) REVERT: B 96 MET cc_start: 0.7960 (ppp) cc_final: 0.7382 (ppp) REVERT: b 284 MET cc_start: 0.8464 (ptp) cc_final: 0.8227 (ptp) REVERT: b 311 ASP cc_start: 0.8992 (m-30) cc_final: 0.8733 (m-30) REVERT: b 410 MET cc_start: 0.9111 (mtt) cc_final: 0.8851 (mtp) REVERT: C 82 MET cc_start: 0.9060 (ptp) cc_final: 0.8657 (pmm) REVERT: C 96 MET cc_start: 0.8162 (ppp) cc_final: 0.7565 (ppp) REVERT: C 116 LYS cc_start: 0.7907 (mttt) cc_final: 0.7294 (tptt) REVERT: C 134 MET cc_start: 0.7314 (ttp) cc_final: 0.6023 (mtt) REVERT: C 200 TYR cc_start: 0.8013 (p90) cc_final: 0.7773 (p90) REVERT: C 217 TYR cc_start: 0.7443 (m-10) cc_final: 0.7225 (m-80) REVERT: c 284 MET cc_start: 0.8376 (ptp) cc_final: 0.8025 (ptp) REVERT: c 311 ASP cc_start: 0.9132 (m-30) cc_final: 0.8771 (m-30) REVERT: c 410 MET cc_start: 0.9033 (mtt) cc_final: 0.8789 (mtp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.0908 time to fit residues: 27.5128 Evaluate side-chains 166 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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: 2.9990 chunk 142 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 150 optimal weight: 50.0000 chunk 82 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.073640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.062277 restraints weight = 78017.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063644 restraints weight = 50929.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.064574 restraints weight = 37530.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.065219 restraints weight = 30411.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.065671 restraints weight = 26284.385| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12339 Z= 0.185 Angle : 0.925 15.264 16953 Z= 0.433 Chirality : 0.048 0.348 2202 Planarity : 0.004 0.049 2070 Dihedral : 5.733 30.202 1689 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.20), residues: 1605 helix: -0.06 (0.27), residues: 327 sheet: -0.70 (0.26), residues: 339 loop : -1.61 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 193 TYR 0.038 0.002 TYR c 371 PHE 0.021 0.002 PHE C 157 TRP 0.024 0.002 TRP A 210 HIS 0.005 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (12231) covalent geometry : angle 0.84838 / 0.42 (16650) SS BOND : bond 0.00323 / 0.21 ( 21) SS BOND : angle 1.55502 / 0.91 ( 42) hydrogen bonds : bond 0.04303 / 2.86 ( 531) hydrogen bonds : angle 5.91973 / 4.18 ( 1458) link_ALPHA1-3 : bond 0.00349 / 0.17 ( 3) link_ALPHA1-3 : angle 3.12688 / 1.57 ( 9) link_ALPHA1-6 : bond 0.01694 / 0.85 ( 3) link_ALPHA1-6 : angle 2.03437 / 1.14 ( 9) link_BETA1-4 : bond 0.00568 / 0.35 ( 42) link_BETA1-4 : angle 1.99575 / 1.44 ( 126) link_BETA1-6 : bond 0.02976 / 1.77 ( 6) link_BETA1-6 : angle 6.45038 / 4.25 ( 18) link_NAG-ASN : bond 0.00277 / 0.20 ( 33) link_NAG-ASN : angle 3.24933 / 2.40 ( 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 195 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.387 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: 0.7648 (mmm) cc_final: 0.7372 (mmm) REVERT: A 96 MET cc_start: 0.8041 (ppp) cc_final: 0.7575 (ppp) REVERT: A 134 MET cc_start: 0.7631 (tmm) cc_final: 0.7070 (ttt) REVERT: a 284 MET cc_start: 0.7647 (pmm) cc_final: 0.7279 (pmm) REVERT: a 308 GLU cc_start: 0.8593 (mp0) cc_final: 0.7846 (mp0) REVERT: a 311 ASP cc_start: 0.9140 (m-30) cc_final: 0.8797 (m-30) REVERT: a 410 MET cc_start: 0.9082 (mtt) cc_final: 0.8790 (mtp) REVERT: B 96 MET cc_start: 0.7860 (ppp) cc_final: 0.7289 (ppp) REVERT: b 284 MET cc_start: 0.8372 (ptp) cc_final: 0.7917 (ptp) REVERT: b 332 MET cc_start: 0.6601 (mtt) cc_final: 0.5667 (mtt) REVERT: b 410 MET cc_start: 0.9091 (mtt) cc_final: 0.8760 (mtp) REVERT: C 73 LEU cc_start: 0.8926 (mt) cc_final: 0.8656 (mt) REVERT: C 75 MET cc_start: 0.7087 (mtp) cc_final: 0.6774 (ttt) REVERT: C 96 MET cc_start: 0.8030 (ppp) cc_final: 0.7411 (ppp) REVERT: C 116 LYS cc_start: 0.7905 (mttt) cc_final: 0.7226 (tptt) REVERT: C 134 MET cc_start: 0.7304 (ttp) cc_final: 0.6094 (mtt) REVERT: C 200 TYR cc_start: 0.8022 (p90) cc_final: 0.7789 (p90) REVERT: C 217 TYR cc_start: 0.7398 (m-10) cc_final: 0.7166 (m-80) REVERT: c 284 MET cc_start: 0.8402 (ptp) cc_final: 0.8050 (ptp) REVERT: c 311 ASP cc_start: 0.9073 (m-30) cc_final: 0.8753 (m-30) REVERT: c 363 TYR cc_start: 0.7402 (p90) cc_final: 0.7145 (p90) REVERT: c 410 MET cc_start: 0.9038 (mtt) cc_final: 0.8796 (mtp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.0862 time to fit residues: 24.8548 Evaluate side-chains 165 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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: 0.8980 chunk 74 optimal weight: 0.8980 chunk 154 optimal weight: 30.0000 chunk 148 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 ASN C 189 GLN c 406 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.075587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064288 restraints weight = 78202.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065661 restraints weight = 51289.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.066622 restraints weight = 37880.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.067308 restraints weight = 30491.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.067703 restraints weight = 26155.513| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.6865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12339 Z= 0.151 Angle : 0.870 14.797 16953 Z= 0.404 Chirality : 0.047 0.353 2202 Planarity : 0.004 0.052 2070 Dihedral : 5.429 28.344 1689 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.12 % Allowed : 0.35 % Favored : 99.53 % 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: -1.38 (0.20), residues: 1605 helix: 0.21 (0.28), residues: 327 sheet: -0.62 (0.26), residues: 342 loop : -1.47 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 193 TYR 0.027 0.002 TYR b 371 PHE 0.043 0.002 PHE A 233 TRP 0.023 0.002 TRP A 227 HIS 0.006 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (12231) covalent geometry : angle 0.79580 / 0.39 (16650) SS BOND : bond 0.00341 / 0.23 ( 21) SS BOND : angle 1.43473 / 0.85 ( 42) hydrogen bonds : bond 0.03890 / 2.58 ( 531) hydrogen bonds : angle 5.61570 / 3.99 ( 1458) link_ALPHA1-3 : bond 0.00382 / 0.19 ( 3) link_ALPHA1-3 : angle 2.99192 / 1.51 ( 9) link_ALPHA1-6 : bond 0.01694 / 0.85 ( 3) link_ALPHA1-6 : angle 2.04906 / 1.13 ( 9) link_BETA1-4 : bond 0.00589 / 0.36 ( 42) link_BETA1-4 : angle 1.90067 / 1.35 ( 126) link_BETA1-6 : bond 0.02991 / 1.76 ( 6) link_BETA1-6 : angle 6.24895 / 4.11 ( 18) link_NAG-ASN : bond 0.00306 / 0.21 ( 33) link_NAG-ASN : angle 3.04911 / 2.26 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1630.98 seconds wall clock time: 29 minutes 15.66 seconds (1755.66 seconds total)