Starting phenix.real_space_refine on Fri Jul 3 15:54:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ejj_28184/07_2026/8ejj_28184.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejj_28184/07_2026/8ejj_28184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ejj_28184/07_2026/8ejj_28184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejj_28184/07_2026/8ejj_28184.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ejj_28184/07_2026/8ejj_28184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejj_28184/07_2026/8ejj_28184.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ejj_28184/07_2026/8ejj_28184.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ejj_28184/07_2026/8ejj_28184.cif" } resolution = 3.22 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= 0.001 sd= 0.029 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 114 5.16 5 C 9276 2.51 5 N 2367 2.21 5 O 3105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 14862 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "I" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "J" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "a" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "b" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "c" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "h" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "l" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "N" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "g" 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: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "k" 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: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "l" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.21, per 1000 atoms: 0.22 Number of scatterers: 14862 At special positions: 0 Unit cell: (131.1, 129.95, 102.35, 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 114 16.00 O 3105 8.00 N 2367 7.00 C 9276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.15 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.15 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.15 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.15 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.02 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 111D" distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.02 Simple disulfide: pdb=" SG CYS I 110 " - pdb=" SG CYS I 111D" distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.02 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=2.01 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=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.01 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=2.01 Simple disulfide: pdb=" SG CYS h 23 " - pdb=" SG CYS h 104 " distance=2.02 Simple disulfide: pdb=" SG CYS h 110 " - pdb=" SG CYS h 111D" distance=2.02 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Z 4 " - " MAN Z 5 " " MAN f 4 " - " MAN f 5 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA D 3 " - " MAN l 201 " " BMA N 3 " - " MAN N 4 " " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " " BMA f 3 " - " MAN f 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " BMA N 3 " - " MAN N 5 " " BMA T 3 " - " MAN T 5 " " BMA Z 3 " - " MAN Z 6 " " BMA f 3 " - " MAN f 6 " " BMA j 3 " - " MAN j 6 " 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 G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG 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 g 2 " - " BMA g 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG m 1 " - " NAG m 2 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG W 1 " - " FUC W 3 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG B 301 " - " ASN B 99 " " NAG C 301 " - " ASN C 99 " " 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 K 1 " - " ASN A 167 " " NAG M 1 " - " ASN A 224 " " NAG N 1 " - " ASN B 79 " " NAG O 1 " - " ASN B 89 " " NAG P 1 " - " ASN B 109 " " NAG Q 1 " - " ASN B 119 " " NAG R 1 " - " ASN B 167 " " NAG S 1 " - " ASN B 224 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 89 " " NAG V 1 " - " ASN C 109 " " NAG W 1 " - " ASN C 119 " " NAG X 1 " - " ASN C 167 " " NAG Y 1 " - " ASN C 224 " " NAG Z 1 " - " ASN a 365 " " NAG a 501 " - " ASN a 395 " " NAG b 501 " - " ASN b 395 " " NAG c 501 " - " ASN c 395 " " NAG d 1 " - " ASN a 373 " " NAG e 1 " - " ASN a 390 " " NAG f 1 " - " ASN b 365 " " NAG g 1 " - " ASN b 373 " " NAG i 1 " - " ASN b 390 " " NAG j 1 " - " ASN c 365 " " NAG k 1 " - " ASN c 373 " " NAG m 1 " - " ASN c 390 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 600.8 milliseconds 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 27 sheets defined 27.9% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 removed outlier: 4.005A pdb=" N ILE A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 183 through 195 removed outlier: 4.215A pdb=" N GLN A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 removed outlier: 4.004A pdb=" N ILE B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 183 through 195 removed outlier: 4.214A pdb=" N GLN B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 removed outlier: 4.006A pdb=" N ILE C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 183 through 195 removed outlier: 4.215A pdb=" N GLN C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'H' and resid 71 through 74 No H-bonds generated for 'chain 'H' and resid 71 through 74' Processing helix chain 'H' and resid 111A through 112 removed outlier: 3.640A pdb=" N CYS H 111D" --> pdb=" O SER H 111A" (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 74 No H-bonds generated for 'chain 'I' and resid 71 through 74' Processing helix chain 'I' and resid 111A through 112 removed outlier: 3.641A pdb=" N CYS I 111D" --> pdb=" O SER I 111A" (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 334 through 345 removed outlier: 5.681A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU a 344 " --> pdb=" O ALA a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.929A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 423 Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 334 through 345 removed outlier: 5.681A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU b 344 " --> pdb=" O ALA b 340 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.930A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 423 Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.681A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU c 344 " --> pdb=" O ALA c 340 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.929A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 423 Processing helix chain 'h' and resid 71 through 74 No H-bonds generated for 'chain 'h' and resid 71 through 74' Processing helix chain 'h' and resid 111A through 112 removed outlier: 3.641A pdb=" N CYS h 111D" --> pdb=" O SER h 111A" (cutoff:3.500A) Processing helix chain 'l' and resid 95 through 99 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 153 through 155 removed outlier: 4.507A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR A 87 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG A 235 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 155 removed outlier: 4.507A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR B 87 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG B 235 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.507A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR C 87 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG C 235 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 12 through 13 removed outlier: 6.105A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 19 through 22 Processing sheet with id=AA9, first strand: chain 'I' and resid 12 through 13 removed outlier: 6.105A pdb=" N ARG I 43 " --> pdb=" O TRP I 52 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP I 52 " --> pdb=" O ARG I 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=AB2, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.546A pdb=" N TRP J 41 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AB4, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.548A pdb=" N TRP L 41 " --> pdb=" O VAL L 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB8, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AB9, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AC1, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AC2, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AC3, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AC4, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AC5, first strand: chain 'h' and resid 12 through 13 removed outlier: 6.106A pdb=" N ARG h 43 " --> pdb=" O TRP h 52 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TRP h 52 " --> pdb=" O ARG h 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 19 through 22 Processing sheet with id=AC7, first strand: chain 'l' and resid 9 through 12 removed outlier: 6.548A pdb=" N TRP l 41 " --> pdb=" O VAL l 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'l' and resid 9 through 12 Processing sheet with id=AC9, first strand: chain 'l' and resid 19 through 24 579 hydrogen bonds defined for protein. 1449 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: 2.54 Time building geometry restraints manager: 2.08 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: 3699 1.33 - 1.47: 5128 1.47 - 1.61: 6185 1.61 - 1.75: 37 1.75 - 1.90: 134 Bond restraints: 15183 Sorted by residual: bond pdb=" CB HIS b 354 " pdb=" CG HIS b 354 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.73e+01 bond pdb=" CB LEU l 127 " pdb=" CG LEU l 127 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" CB HIS a 354 " pdb=" CG HIS a 354 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" CB HIS A 141 " pdb=" CG HIS A 141 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.66e+01 bond pdb=" CB LEU L 127 " pdb=" CG LEU L 127 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 15178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 17471 2.38 - 4.76: 2637 4.76 - 7.14: 422 7.14 - 9.51: 65 9.51 - 11.89: 12 Bond angle restraints: 20607 Sorted by residual: angle pdb=" N PRO H 45 " pdb=" CA PRO H 45 " pdb=" C PRO H 45 " ideal model delta sigma weight residual 110.47 102.96 7.51 9.60e-01 1.09e+00 6.12e+01 angle pdb=" N VAL H 76 " pdb=" CA VAL H 76 " pdb=" C VAL H 76 " ideal model delta sigma weight residual 108.11 118.92 -10.81 1.40e+00 5.10e-01 5.96e+01 angle pdb=" N PRO I 45 " pdb=" CA PRO I 45 " pdb=" C PRO I 45 " ideal model delta sigma weight residual 110.47 103.07 7.40 9.60e-01 1.09e+00 5.93e+01 angle pdb=" N PRO h 45 " pdb=" CA PRO h 45 " pdb=" C PRO h 45 " ideal model delta sigma weight residual 110.47 103.09 7.38 9.60e-01 1.09e+00 5.92e+01 angle pdb=" N VAL I 76 " pdb=" CA VAL I 76 " pdb=" C VAL I 76 " ideal model delta sigma weight residual 108.11 118.85 -10.74 1.40e+00 5.10e-01 5.88e+01 ... (remaining 20602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 7953 14.77 - 29.55: 318 29.55 - 44.32: 60 44.32 - 59.09: 54 59.09 - 73.87: 21 Dihedral angle restraints: 8406 sinusoidal: 3336 harmonic: 5070 Sorted by residual: dihedral pdb=" CB CYS B 180 " pdb=" SG CYS B 180 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -26.46 -59.54 1 1.00e+01 1.00e-02 4.73e+01 dihedral pdb=" CB CYS A 180 " pdb=" SG CYS A 180 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual -86.00 -26.61 -59.39 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS C 180 " pdb=" SG CYS C 180 " pdb=" SG CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sinusoidal sigma weight residual -86.00 -26.67 -59.33 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 8403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1552 0.103 - 0.206: 591 0.206 - 0.309: 225 0.309 - 0.412: 114 0.412 - 0.516: 38 Chirality restraints: 2520 Sorted by residual: chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 BMA g 3 " pdb=" O4 NAG g 2 " pdb=" C2 BMA g 3 " pdb=" O5 BMA g 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+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 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 2517 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 89 " -0.056 2.00e-02 2.50e+03 5.76e-02 4.14e+01 pdb=" CG ASN C 89 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 89 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 89 " 0.088 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 89 " 0.056 2.00e-02 2.50e+03 5.74e-02 4.12e+01 pdb=" CG ASN B 89 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 89 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 89 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 89 " -0.056 2.00e-02 2.50e+03 5.72e-02 4.09e+01 pdb=" CG ASN A 89 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 89 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 89 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.069 2.00e-02 2.50e+03 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 5960 2.90 - 3.40: 13477 3.40 - 3.90: 25244 3.90 - 4.40: 29786 4.40 - 4.90: 47733 Nonbonded interactions: 122200 Sorted by model distance: nonbonded pdb=" OH TYR h 38 " pdb=" O CYS h 111D" model vdw 2.394 3.040 nonbonded pdb=" OH TYR H 38 " pdb=" O CYS H 111D" model vdw 2.394 3.040 nonbonded pdb=" OH TYR I 38 " pdb=" O CYS I 111D" model vdw 2.394 3.040 nonbonded pdb=" O4 MAN j 4 " pdb=" O6 MAN j 4 " model vdw 2.395 3.040 nonbonded pdb=" O4 MAN Z 4 " pdb=" O6 MAN Z 4 " model vdw 2.396 3.040 ... (remaining 122195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'e' selection = chain 'i' selection = chain 'm' } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'h' } ncs_group { reference = chain 'J' selection = chain 'L' selection = (chain 'l' and resid 2 through 127) } ncs_group { reference = chain 'N' selection = chain 'T' } ncs_group { reference = chain 'Z' selection = chain 'f' selection = chain 'j' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.410 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.138 15300 Z= 1.286 Angle : 2.018 53.110 20928 Z= 1.213 Chirality : 0.146 0.516 2520 Planarity : 0.009 0.079 2490 Dihedral : 9.986 73.868 5076 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1713 helix: -1.15 (0.23), residues: 369 sheet: 0.95 (0.26), residues: 450 loop : 0.56 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 75 TYR 0.063 0.008 TYR H 26 PHE 0.030 0.007 PHE h 115 TRP 0.039 0.010 TRP H 52 HIS 0.010 0.002 HIS c 354 Details of bonding type rmsd/Z covalent geometry : bond 0.02410 / 1.26 (15183) covalent geometry : angle 1.79681 / 1.15 (20607) SS BOND : bond 0.04519 / 2.73 ( 30) SS BOND : angle 14.77117 / 7.33 ( 60) hydrogen bonds : bond 0.16883 / 11.12 ( 561) hydrogen bonds : angle 7.46701 / 5.18 ( 1449) link_ALPHA1-2 : bond 0.07680 / 3.54 ( 3) link_ALPHA1-2 : angle 4.68004 / 2.70 ( 9) link_ALPHA1-3 : bond 0.09704 / 5.21 ( 6) link_ALPHA1-3 : angle 7.27547 / 4.90 ( 18) link_ALPHA1-6 : bond 0.05442 / 2.87 ( 6) link_ALPHA1-6 : angle 3.58101 / 2.27 ( 18) link_BETA1-4 : bond 0.06988 / 4.40 ( 36) link_BETA1-4 : angle 5.72432 / 3.77 ( 108) link_BETA1-6 : bond 0.05237 / 2.42 ( 3) link_BETA1-6 : angle 2.32469 / 1.34 ( 9) link_NAG-ASN : bond 0.07143 / 4.44 ( 33) link_NAG-ASN : angle 2.58794 / 1.59 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8969 (mmp) cc_final: 0.8744 (mmt) REVERT: A 115 HIS cc_start: 0.7304 (m170) cc_final: 0.7102 (m90) REVERT: B 115 HIS cc_start: 0.7382 (m170) cc_final: 0.7135 (m-70) REVERT: J 67 ARG cc_start: 0.8902 (ttp-110) cc_final: 0.8507 (ttm110) REVERT: L 67 ARG cc_start: 0.8766 (ttp-110) cc_final: 0.8438 (ttm110) REVERT: c 332 MET cc_start: 0.8178 (tmt) cc_final: 0.7120 (tmt) REVERT: c 401 ASP cc_start: 0.7665 (m-30) cc_final: 0.7438 (m-30) REVERT: c 410 MET cc_start: 0.8516 (mtp) cc_final: 0.8222 (mtp) REVERT: c 419 TYR cc_start: 0.8216 (t80) cc_final: 0.7967 (t80) REVERT: l 18 THR cc_start: 0.8356 (m) cc_final: 0.8040 (p) REVERT: l 67 ARG cc_start: 0.8784 (ttp-110) cc_final: 0.8213 (ttm110) REVERT: l 123 LYS cc_start: 0.8313 (ttmm) cc_final: 0.8031 (ttmm) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1539 time to fit residues: 78.1370 Evaluate side-chains 197 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 58 HIS ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 354 HIS ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 324 GLN ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 324 GLN h 58 HIS ** l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.103222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086339 restraints weight = 27716.615| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.43 r_work: 0.3271 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 15300 Z= 0.186 Angle : 0.814 10.790 20928 Z= 0.397 Chirality : 0.048 0.256 2520 Planarity : 0.005 0.045 2490 Dihedral : 5.244 18.580 1890 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.49 % Allowed : 6.76 % Favored : 91.75 % 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: 0.64 (0.21), residues: 1713 helix: 0.34 (0.26), residues: 366 sheet: 1.02 (0.26), residues: 432 loop : 0.29 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG l 67 TYR 0.019 0.002 TYR L 115 PHE 0.018 0.002 PHE A 117 TRP 0.027 0.002 TRP C 210 HIS 0.004 0.001 HIS c 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (15183) covalent geometry : angle 0.74385 / 0.38 (20607) SS BOND : bond 0.00419 / 0.27 ( 30) SS BOND : angle 1.44058 / 0.88 ( 60) hydrogen bonds : bond 0.05235 / 3.47 ( 561) hydrogen bonds : angle 5.51694 / 3.87 ( 1449) link_ALPHA1-2 : bond 0.00061 / 0.03 ( 3) link_ALPHA1-2 : angle 2.10241 / 1.20 ( 9) link_ALPHA1-3 : bond 0.02436 / 1.17 ( 6) link_ALPHA1-3 : angle 3.76052 / 2.50 ( 18) link_ALPHA1-6 : bond 0.00907 / 0.45 ( 6) link_ALPHA1-6 : angle 1.20178 / 0.75 ( 18) link_BETA1-4 : bond 0.00748 / 0.48 ( 36) link_BETA1-4 : angle 3.60142 / 2.39 ( 108) link_BETA1-6 : bond 0.00174 / 0.08 ( 3) link_BETA1-6 : angle 1.47356 / 0.77 ( 9) link_NAG-ASN : bond 0.00491 / 0.33 ( 33) link_NAG-ASN : angle 2.49239 / 1.56 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7376 (m170) cc_final: 0.7154 (m90) REVERT: A 122 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8461 (m-30) REVERT: A 204 ASP cc_start: 0.8514 (t0) cc_final: 0.8259 (t0) REVERT: B 75 MET cc_start: 0.8848 (mtm) cc_final: 0.8600 (mtp) REVERT: B 115 HIS cc_start: 0.7380 (m170) cc_final: 0.6992 (m90) REVERT: B 151 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: C 180 CYS cc_start: 0.5495 (OUTLIER) cc_final: 0.5130 (t) REVERT: C 204 ASP cc_start: 0.8693 (t0) cc_final: 0.8290 (t0) REVERT: C 211 ASP cc_start: 0.7008 (p0) cc_final: 0.6652 (t0) REVERT: J 123 LYS cc_start: 0.8364 (tttt) cc_final: 0.8059 (mttp) REVERT: L 67 ARG cc_start: 0.8903 (ttp-110) cc_final: 0.8599 (ttm110) REVERT: L 123 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8260 (ttmm) REVERT: b 306 ASP cc_start: 0.8571 (p0) cc_final: 0.8349 (p0) REVERT: b 332 MET cc_start: 0.8207 (tmt) cc_final: 0.7942 (tmm) REVERT: b 333 SER cc_start: 0.7882 (t) cc_final: 0.7436 (p) REVERT: b 379 ARG cc_start: 0.8627 (ttm-80) cc_final: 0.8273 (mmm-85) REVERT: l 123 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8199 (mmtm) outliers start: 23 outliers final: 12 residues processed: 256 average time/residue: 0.1287 time to fit residues: 46.8980 Evaluate side-chains 219 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain b residue 283 TRP Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS B 93 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 115 HIS C 185 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071510 restraints weight = 28286.186| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.71 r_work: 0.2910 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 15300 Z= 0.209 Angle : 0.756 8.704 20928 Z= 0.365 Chirality : 0.046 0.255 2520 Planarity : 0.005 0.044 2490 Dihedral : 4.952 23.511 1890 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.82 % Allowed : 8.25 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 1713 helix: 0.89 (0.27), residues: 372 sheet: 0.91 (0.25), residues: 432 loop : -0.21 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 379 TYR 0.018 0.002 TYR h 26 PHE 0.020 0.002 PHE A 117 TRP 0.039 0.002 TRP B 210 HIS 0.012 0.002 HIS B 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (15183) covalent geometry : angle 0.69544 / 0.35 (20607) SS BOND : bond 0.00592 / 0.36 ( 30) SS BOND : angle 1.82592 / 1.25 ( 60) hydrogen bonds : bond 0.04578 / 3.02 ( 561) hydrogen bonds : angle 5.12327 / 3.62 ( 1449) link_ALPHA1-2 : bond 0.00088 / 0.04 ( 3) link_ALPHA1-2 : angle 2.06976 / 1.15 ( 9) link_ALPHA1-3 : bond 0.02207 / 1.07 ( 6) link_ALPHA1-3 : angle 3.70032 / 2.46 ( 18) link_ALPHA1-6 : bond 0.00565 / 0.27 ( 6) link_ALPHA1-6 : angle 1.48571 / 0.87 ( 18) link_BETA1-4 : bond 0.00710 / 0.46 ( 36) link_BETA1-4 : angle 2.88214 / 1.96 ( 108) link_BETA1-6 : bond 0.00271 / 0.13 ( 3) link_BETA1-6 : angle 1.53023 / 0.78 ( 9) link_NAG-ASN : bond 0.00358 / 0.23 ( 33) link_NAG-ASN : angle 2.34962 / 1.45 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7222 (m170) cc_final: 0.6974 (m90) REVERT: A 204 ASP cc_start: 0.8552 (t0) cc_final: 0.8229 (t0) REVERT: B 115 HIS cc_start: 0.7303 (m170) cc_final: 0.6895 (m90) REVERT: C 75 MET cc_start: 0.9116 (mtm) cc_final: 0.8911 (mtm) REVERT: C 115 HIS cc_start: 0.7095 (m170) cc_final: 0.6865 (m90) REVERT: C 204 ASP cc_start: 0.8474 (t0) cc_final: 0.8140 (t0) REVERT: I 48 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8345 (mttm) REVERT: J 123 LYS cc_start: 0.8433 (tttt) cc_final: 0.8134 (mttp) REVERT: L 123 LYS cc_start: 0.8410 (ttmm) cc_final: 0.8093 (ttmm) REVERT: a 306 ASP cc_start: 0.8666 (p0) cc_final: 0.8391 (p0) REVERT: b 379 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8244 (mmm-85) REVERT: c 410 MET cc_start: 0.8540 (mtp) cc_final: 0.8225 (mtp) REVERT: l 123 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8068 (mmtm) outliers start: 28 outliers final: 19 residues processed: 214 average time/residue: 0.1319 time to fit residues: 40.9087 Evaluate side-chains 198 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 51 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 56 optimal weight: 0.0970 chunk 118 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 66 ASN ** 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 = 0.3423 r_free = 0.3423 target = 0.092485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.074073 restraints weight = 27966.938| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.64 r_work: 0.2934 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15300 Z= 0.126 Angle : 0.658 8.273 20928 Z= 0.314 Chirality : 0.043 0.235 2520 Planarity : 0.004 0.044 2490 Dihedral : 4.700 22.183 1890 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.69 % Allowed : 9.36 % Favored : 88.95 % 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: 0.40 (0.20), residues: 1713 helix: 1.19 (0.27), residues: 372 sheet: 0.85 (0.25), residues: 435 loop : -0.38 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 379 TYR 0.016 0.001 TYR b 419 PHE 0.010 0.001 PHE A 117 TRP 0.038 0.001 TRP C 210 HIS 0.010 0.001 HIS C 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (15183) covalent geometry : angle 0.60200 / 0.30 (20607) SS BOND : bond 0.00358 / 0.18 ( 30) SS BOND : angle 1.83820 / 1.09 ( 60) hydrogen bonds : bond 0.03675 / 2.43 ( 561) hydrogen bonds : angle 4.86775 / 3.43 ( 1449) link_ALPHA1-2 : bond 0.00067 / 0.03 ( 3) link_ALPHA1-2 : angle 1.84804 / 1.00 ( 9) link_ALPHA1-3 : bond 0.01983 / 0.95 ( 6) link_ALPHA1-3 : angle 3.34156 / 2.20 ( 18) link_ALPHA1-6 : bond 0.00616 / 0.30 ( 6) link_ALPHA1-6 : angle 1.34266 / 0.79 ( 18) link_BETA1-4 : bond 0.00631 / 0.40 ( 36) link_BETA1-4 : angle 2.50103 / 1.71 ( 108) link_BETA1-6 : bond 0.00227 / 0.10 ( 3) link_BETA1-6 : angle 1.53009 / 0.78 ( 9) link_NAG-ASN : bond 0.00306 / 0.21 ( 33) link_NAG-ASN : angle 2.11184 / 1.30 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7813 (pt0) REVERT: A 204 ASP cc_start: 0.8524 (t0) cc_final: 0.8182 (t0) REVERT: B 115 HIS cc_start: 0.7059 (m170) cc_final: 0.6669 (m90) REVERT: C 115 HIS cc_start: 0.6878 (m170) cc_final: 0.6673 (m90) REVERT: C 204 ASP cc_start: 0.8583 (t0) cc_final: 0.8280 (t0) REVERT: J 123 LYS cc_start: 0.8450 (tttt) cc_final: 0.8128 (mttp) REVERT: L 123 LYS cc_start: 0.8343 (ttmm) cc_final: 0.7961 (mttm) REVERT: b 379 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8324 (mmm-85) REVERT: c 324 GLN cc_start: 0.8774 (mt0) cc_final: 0.8432 (mt0) REVERT: c 410 MET cc_start: 0.8478 (mtp) cc_final: 0.7780 (mtp) REVERT: h 94 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8432 (p) REVERT: l 123 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8022 (mmtm) outliers start: 26 outliers final: 16 residues processed: 223 average time/residue: 0.1271 time to fit residues: 42.4130 Evaluate side-chains 204 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 81 optimal weight: 0.0060 chunk 117 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.095982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.077804 restraints weight = 27933.747| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.59 r_work: 0.3064 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15300 Z= 0.129 Angle : 0.660 9.485 20928 Z= 0.315 Chirality : 0.042 0.214 2520 Planarity : 0.004 0.044 2490 Dihedral : 4.611 31.056 1890 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.95 % Allowed : 10.27 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1713 helix: 1.44 (0.28), residues: 369 sheet: 0.74 (0.25), residues: 441 loop : -0.43 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 379 TYR 0.015 0.001 TYR b 419 PHE 0.010 0.001 PHE A 117 TRP 0.018 0.001 TRP C 210 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (15183) covalent geometry : angle 0.60408 / 0.30 (20607) SS BOND : bond 0.00440 / 0.25 ( 30) SS BOND : angle 2.07053 / 1.23 ( 60) hydrogen bonds : bond 0.03552 / 2.33 ( 561) hydrogen bonds : angle 4.79229 / 3.37 ( 1449) link_ALPHA1-2 : bond 0.00081 / 0.04 ( 3) link_ALPHA1-2 : angle 1.81868 / 0.98 ( 9) link_ALPHA1-3 : bond 0.01916 / 0.93 ( 6) link_ALPHA1-3 : angle 3.35162 / 2.20 ( 18) link_ALPHA1-6 : bond 0.00595 / 0.29 ( 6) link_ALPHA1-6 : angle 1.36608 / 0.81 ( 18) link_BETA1-4 : bond 0.00622 / 0.40 ( 36) link_BETA1-4 : angle 2.40394 / 1.64 ( 108) link_BETA1-6 : bond 0.00261 / 0.12 ( 3) link_BETA1-6 : angle 1.51536 / 0.77 ( 9) link_NAG-ASN : bond 0.00293 / 0.20 ( 33) link_NAG-ASN : angle 2.08359 / 1.29 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.564 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 151 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: A 204 ASP cc_start: 0.8530 (t0) cc_final: 0.8154 (t0) REVERT: A 211 ASP cc_start: 0.7557 (p0) cc_final: 0.7352 (t0) REVERT: B 115 HIS cc_start: 0.7142 (m170) cc_final: 0.6713 (m90) REVERT: C 204 ASP cc_start: 0.8630 (t0) cc_final: 0.8394 (t0) REVERT: H 14 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7474 (mmtt) REVERT: I 17 GLU cc_start: 0.8761 (pt0) cc_final: 0.8557 (pm20) REVERT: J 123 LYS cc_start: 0.8555 (tttt) cc_final: 0.8234 (mttp) REVERT: L 123 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8117 (mttm) REVERT: b 379 ARG cc_start: 0.8745 (ttm-80) cc_final: 0.8504 (mmm-85) REVERT: b 420 MET cc_start: 0.8771 (mmm) cc_final: 0.8291 (tmm) REVERT: c 324 GLN cc_start: 0.8871 (mt0) cc_final: 0.8577 (mt0) outliers start: 30 outliers final: 21 residues processed: 213 average time/residue: 0.1334 time to fit residues: 41.7983 Evaluate side-chains 207 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 65 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 141 HIS C 189 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.093524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.075125 restraints weight = 27921.814| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.60 r_work: 0.3011 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 15300 Z= 0.197 Angle : 0.708 11.206 20928 Z= 0.337 Chirality : 0.045 0.221 2520 Planarity : 0.005 0.049 2490 Dihedral : 4.700 26.422 1890 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.47 % Allowed : 10.01 % Favored : 87.52 % 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: 0.24 (0.20), residues: 1713 helix: 1.43 (0.28), residues: 369 sheet: 0.67 (0.25), residues: 435 loop : -0.61 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 379 TYR 0.016 0.001 TYR b 419 PHE 0.019 0.001 PHE A 117 TRP 0.035 0.002 TRP B 210 HIS 0.013 0.001 HIS C 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (15183) covalent geometry : angle 0.65414 / 0.32 (20607) SS BOND : bond 0.00593 / 0.38 ( 30) SS BOND : angle 2.07243 / 1.23 ( 60) hydrogen bonds : bond 0.03827 / 2.51 ( 561) hydrogen bonds : angle 4.87713 / 3.44 ( 1449) link_ALPHA1-2 : bond 0.00252 / 0.12 ( 3) link_ALPHA1-2 : angle 1.91520 / 1.04 ( 9) link_ALPHA1-3 : bond 0.01849 / 0.89 ( 6) link_ALPHA1-3 : angle 3.29424 / 2.17 ( 18) link_ALPHA1-6 : bond 0.00522 / 0.25 ( 6) link_ALPHA1-6 : angle 1.49508 / 0.89 ( 18) link_BETA1-4 : bond 0.00552 / 0.36 ( 36) link_BETA1-4 : angle 2.41406 / 1.63 ( 108) link_BETA1-6 : bond 0.00218 / 0.10 ( 3) link_BETA1-6 : angle 1.57741 / 0.81 ( 9) link_NAG-ASN : bond 0.00324 / 0.21 ( 33) link_NAG-ASN : angle 2.20469 / 1.35 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8544 (t0) cc_final: 0.8145 (t0) REVERT: B 115 HIS cc_start: 0.7286 (m170) cc_final: 0.6875 (m90) REVERT: B 151 GLU cc_start: 0.8186 (pt0) cc_final: 0.7808 (pm20) REVERT: C 204 ASP cc_start: 0.8650 (t0) cc_final: 0.8439 (t0) REVERT: I 48 LYS cc_start: 0.8840 (mttp) cc_final: 0.8574 (mttm) REVERT: J 123 LYS cc_start: 0.8571 (tttt) cc_final: 0.8258 (mttp) REVERT: L 123 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8025 (mttm) REVERT: a 306 ASP cc_start: 0.8868 (p0) cc_final: 0.8614 (p0) REVERT: b 379 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.8454 (mmm-85) REVERT: c 332 MET cc_start: 0.8350 (tmt) cc_final: 0.7758 (tmt) REVERT: l 123 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8114 (mttm) outliers start: 38 outliers final: 30 residues processed: 211 average time/residue: 0.1303 time to fit residues: 40.5460 Evaluate side-chains 206 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 11 optimal weight: 0.0670 chunk 166 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.095304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.077059 restraints weight = 27401.621| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.57 r_work: 0.3051 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15300 Z= 0.122 Angle : 0.639 9.241 20928 Z= 0.303 Chirality : 0.042 0.195 2520 Planarity : 0.004 0.047 2490 Dihedral : 4.501 23.255 1890 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.95 % Allowed : 10.20 % Favored : 87.85 % 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: 0.27 (0.20), residues: 1713 helix: 1.62 (0.28), residues: 369 sheet: 0.50 (0.25), residues: 417 loop : -0.55 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG c 379 TYR 0.010 0.001 TYR L 55 PHE 0.009 0.001 PHE A 117 TRP 0.045 0.001 TRP A 210 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15183) covalent geometry : angle 0.59062 / 0.29 (20607) SS BOND : bond 0.00326 / 0.20 ( 30) SS BOND : angle 1.63566 / 0.95 ( 60) hydrogen bonds : bond 0.03345 / 2.19 ( 561) hydrogen bonds : angle 4.73993 / 3.34 ( 1449) link_ALPHA1-2 : bond 0.00097 / 0.05 ( 3) link_ALPHA1-2 : angle 1.83954 / 0.99 ( 9) link_ALPHA1-3 : bond 0.01763 / 0.87 ( 6) link_ALPHA1-3 : angle 3.17959 / 2.09 ( 18) link_ALPHA1-6 : bond 0.00585 / 0.29 ( 6) link_ALPHA1-6 : angle 1.38151 / 0.80 ( 18) link_BETA1-4 : bond 0.00580 / 0.37 ( 36) link_BETA1-4 : angle 2.23427 / 1.52 ( 108) link_BETA1-6 : bond 0.00184 / 0.09 ( 3) link_BETA1-6 : angle 1.61622 / 0.82 ( 9) link_NAG-ASN : bond 0.00284 / 0.19 ( 33) link_NAG-ASN : angle 2.00973 / 1.24 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8309 (pt0) cc_final: 0.7758 (pm20) REVERT: A 204 ASP cc_start: 0.8525 (t0) cc_final: 0.8195 (t0) REVERT: B 115 HIS cc_start: 0.7271 (m170) cc_final: 0.6866 (m90) REVERT: B 151 GLU cc_start: 0.8180 (pt0) cc_final: 0.7819 (pm20) REVERT: J 123 LYS cc_start: 0.8593 (tttt) cc_final: 0.8280 (mttp) REVERT: L 123 LYS cc_start: 0.8403 (ttmm) cc_final: 0.7985 (mttm) REVERT: b 379 ARG cc_start: 0.8709 (ttm-80) cc_final: 0.8482 (mmm-85) REVERT: c 332 MET cc_start: 0.8394 (tmt) cc_final: 0.7815 (tmt) REVERT: c 401 ASP cc_start: 0.8456 (m-30) cc_final: 0.8148 (m-30) REVERT: l 123 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8068 (mttm) outliers start: 30 outliers final: 25 residues processed: 207 average time/residue: 0.1250 time to fit residues: 38.2413 Evaluate side-chains 207 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.076245 restraints weight = 27827.928| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.57 r_work: 0.3000 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15300 Z= 0.170 Angle : 0.670 8.288 20928 Z= 0.318 Chirality : 0.043 0.198 2520 Planarity : 0.005 0.052 2490 Dihedral : 4.504 22.379 1890 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.14 % Allowed : 10.46 % Favored : 87.39 % 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: 0.16 (0.20), residues: 1713 helix: 1.51 (0.28), residues: 372 sheet: 0.74 (0.26), residues: 408 loop : -0.78 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 379 TYR 0.013 0.001 TYR h 38 PHE 0.014 0.001 PHE A 117 TRP 0.036 0.001 TRP A 210 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (15183) covalent geometry : angle 0.62197 / 0.31 (20607) SS BOND : bond 0.00421 / 0.24 ( 30) SS BOND : angle 1.62297 / 0.97 ( 60) hydrogen bonds : bond 0.03568 / 2.34 ( 561) hydrogen bonds : angle 4.77183 / 3.37 ( 1449) link_ALPHA1-2 : bond 0.00203 / 0.10 ( 3) link_ALPHA1-2 : angle 1.88272 / 1.01 ( 9) link_ALPHA1-3 : bond 0.01728 / 0.84 ( 6) link_ALPHA1-3 : angle 3.11449 / 2.05 ( 18) link_ALPHA1-6 : bond 0.00532 / 0.25 ( 6) link_ALPHA1-6 : angle 1.46602 / 0.87 ( 18) link_BETA1-4 : bond 0.00538 / 0.35 ( 36) link_BETA1-4 : angle 2.26386 / 1.53 ( 108) link_BETA1-6 : bond 0.00184 / 0.08 ( 3) link_BETA1-6 : angle 1.65072 / 0.84 ( 9) link_NAG-ASN : bond 0.00291 / 0.19 ( 33) link_NAG-ASN : angle 2.09141 / 1.29 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8123 (pt0) cc_final: 0.7588 (pm20) REVERT: A 204 ASP cc_start: 0.8473 (t0) cc_final: 0.8109 (t0) REVERT: B 115 HIS cc_start: 0.7253 (m170) cc_final: 0.6867 (m90) REVERT: B 151 GLU cc_start: 0.8023 (pt0) cc_final: 0.7710 (pm20) REVERT: J 123 LYS cc_start: 0.8424 (tttt) cc_final: 0.8114 (mttp) REVERT: L 123 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7875 (mttm) REVERT: b 356 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8134 (mtt180) REVERT: b 379 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8326 (mmm-85) REVERT: c 332 MET cc_start: 0.8235 (tmt) cc_final: 0.7835 (tmt) REVERT: c 401 ASP cc_start: 0.8303 (m-30) cc_final: 0.8009 (m-30) REVERT: l 3 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8246 (pt0) REVERT: l 123 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8004 (mttm) outliers start: 33 outliers final: 25 residues processed: 205 average time/residue: 0.1243 time to fit residues: 37.7059 Evaluate side-chains 204 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 15 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 chunk 152 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.094816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.076474 restraints weight = 27770.924| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.60 r_work: 0.3036 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15300 Z= 0.133 Angle : 0.640 7.631 20928 Z= 0.303 Chirality : 0.042 0.189 2520 Planarity : 0.005 0.053 2490 Dihedral : 4.408 21.510 1890 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.08 % Allowed : 10.66 % Favored : 87.26 % 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: 0.18 (0.20), residues: 1713 helix: 1.54 (0.28), residues: 372 sheet: 0.80 (0.26), residues: 408 loop : -0.80 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG c 379 TYR 0.010 0.001 TYR L 55 PHE 0.010 0.001 PHE A 117 TRP 0.037 0.001 TRP A 210 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (15183) covalent geometry : angle 0.59513 / 0.29 (20607) SS BOND : bond 0.00340 / 0.20 ( 30) SS BOND : angle 1.45709 / 0.86 ( 60) hydrogen bonds : bond 0.03332 / 2.18 ( 561) hydrogen bonds : angle 4.70993 / 3.32 ( 1449) link_ALPHA1-2 : bond 0.00138 / 0.07 ( 3) link_ALPHA1-2 : angle 1.84682 / 0.99 ( 9) link_ALPHA1-3 : bond 0.01656 / 0.82 ( 6) link_ALPHA1-3 : angle 3.01105 / 1.97 ( 18) link_ALPHA1-6 : bond 0.00562 / 0.27 ( 6) link_ALPHA1-6 : angle 1.40670 / 0.82 ( 18) link_BETA1-4 : bond 0.00546 / 0.35 ( 36) link_BETA1-4 : angle 2.16034 / 1.47 ( 108) link_BETA1-6 : bond 0.00164 / 0.08 ( 3) link_BETA1-6 : angle 1.65460 / 0.84 ( 9) link_NAG-ASN : bond 0.00267 / 0.18 ( 33) link_NAG-ASN : angle 1.98751 / 1.22 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8386 (pt0) cc_final: 0.7918 (pm20) REVERT: A 204 ASP cc_start: 0.8579 (t0) cc_final: 0.8212 (t0) REVERT: B 115 HIS cc_start: 0.7168 (m170) cc_final: 0.6775 (m90) REVERT: B 151 GLU cc_start: 0.8261 (pt0) cc_final: 0.7919 (pm20) REVERT: C 151 GLU cc_start: 0.8247 (pt0) cc_final: 0.7734 (pm20) REVERT: J 123 LYS cc_start: 0.8589 (tttt) cc_final: 0.8289 (mttp) REVERT: L 123 LYS cc_start: 0.8413 (ttmm) cc_final: 0.7967 (mttm) REVERT: b 356 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8247 (mtt180) REVERT: b 379 ARG cc_start: 0.8769 (ttm-80) cc_final: 0.8562 (mmm-85) REVERT: b 420 MET cc_start: 0.8081 (mmp) cc_final: 0.7626 (tmm) REVERT: c 332 MET cc_start: 0.8244 (tmt) cc_final: 0.7879 (tmt) REVERT: c 379 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8223 (mtp85) REVERT: c 401 ASP cc_start: 0.8517 (m-30) cc_final: 0.8208 (m-30) REVERT: c 410 MET cc_start: 0.8487 (mtp) cc_final: 0.8234 (mtp) REVERT: l 3 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: l 123 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8128 (mttm) outliers start: 32 outliers final: 27 residues processed: 210 average time/residue: 0.1247 time to fit residues: 38.6765 Evaluate side-chains 207 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 52 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 161 optimal weight: 0.0770 chunk 39 optimal weight: 5.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.093686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.075206 restraints weight = 27872.883| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.63 r_work: 0.3012 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 15300 Z= 0.167 Angle : 0.670 8.002 20928 Z= 0.317 Chirality : 0.043 0.196 2520 Planarity : 0.005 0.056 2490 Dihedral : 4.427 21.323 1890 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.27 % Rotamer: Outliers : 2.08 % Allowed : 10.53 % Favored : 87.39 % 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: 0.08 (0.20), residues: 1713 helix: 1.38 (0.27), residues: 372 sheet: 0.75 (0.26), residues: 408 loop : -0.84 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 379 TYR 0.013 0.001 TYR l 55 PHE 0.013 0.001 PHE A 117 TRP 0.033 0.001 TRP C 210 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (15183) covalent geometry : angle 0.62560 / 0.31 (20607) SS BOND : bond 0.00395 / 0.22 ( 30) SS BOND : angle 1.54569 / 0.92 ( 60) hydrogen bonds : bond 0.03500 / 2.29 ( 561) hydrogen bonds : angle 4.74877 / 3.35 ( 1449) link_ALPHA1-2 : bond 0.00257 / 0.12 ( 3) link_ALPHA1-2 : angle 1.86977 / 1.00 ( 9) link_ALPHA1-3 : bond 0.01602 / 0.79 ( 6) link_ALPHA1-3 : angle 2.95845 / 1.94 ( 18) link_ALPHA1-6 : bond 0.00524 / 0.25 ( 6) link_ALPHA1-6 : angle 1.46222 / 0.86 ( 18) link_BETA1-4 : bond 0.00521 / 0.33 ( 36) link_BETA1-4 : angle 2.18752 / 1.48 ( 108) link_BETA1-6 : bond 0.00154 / 0.07 ( 3) link_BETA1-6 : angle 1.68446 / 0.86 ( 9) link_NAG-ASN : bond 0.00291 / 0.19 ( 33) link_NAG-ASN : angle 2.04772 / 1.26 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8396 (pt0) cc_final: 0.7887 (pm20) REVERT: A 204 ASP cc_start: 0.8601 (t0) cc_final: 0.8242 (t0) REVERT: B 151 GLU cc_start: 0.8286 (pt0) cc_final: 0.7940 (pm20) REVERT: C 151 GLU cc_start: 0.8249 (pt0) cc_final: 0.7747 (pm20) REVERT: J 123 LYS cc_start: 0.8589 (tttt) cc_final: 0.8292 (mttp) REVERT: L 123 LYS cc_start: 0.8418 (ttmm) cc_final: 0.7957 (mttm) REVERT: b 356 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8281 (mtt180) REVERT: b 379 ARG cc_start: 0.8760 (ttm-80) cc_final: 0.8549 (mmm-85) REVERT: b 419 TYR cc_start: 0.8739 (t80) cc_final: 0.8458 (t80) REVERT: b 420 MET cc_start: 0.8141 (mmp) cc_final: 0.7651 (tmm) REVERT: c 332 MET cc_start: 0.8256 (tmt) cc_final: 0.7885 (tmt) REVERT: c 401 ASP cc_start: 0.8562 (m-30) cc_final: 0.8226 (m-30) REVERT: c 410 MET cc_start: 0.8518 (mtp) cc_final: 0.8233 (mtp) REVERT: c 420 MET cc_start: 0.8288 (mmp) cc_final: 0.7897 (tmm) REVERT: l 3 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8411 (pt0) REVERT: l 123 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8042 (mttm) outliers start: 32 outliers final: 29 residues processed: 209 average time/residue: 0.1304 time to fit residues: 40.2331 Evaluate side-chains 210 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 165 optimal weight: 0.0670 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 321 GLN ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.094028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.075787 restraints weight = 27747.106| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.59 r_work: 0.3027 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15300 Z= 0.141 Angle : 0.655 8.038 20928 Z= 0.311 Chirality : 0.042 0.192 2520 Planarity : 0.005 0.059 2490 Dihedral : 4.440 20.737 1890 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 2.34 % Allowed : 10.72 % Favored : 86.94 % 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: 0.08 (0.20), residues: 1713 helix: 1.42 (0.27), residues: 372 sheet: 0.67 (0.27), residues: 384 loop : -0.77 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 379 TYR 0.013 0.001 TYR l 55 PHE 0.011 0.001 PHE A 117 TRP 0.060 0.002 TRP B 210 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (15183) covalent geometry : angle 0.61189 / 0.30 (20607) SS BOND : bond 0.00349 / 0.21 ( 30) SS BOND : angle 1.42783 / 0.83 ( 60) hydrogen bonds : bond 0.03419 / 2.23 ( 561) hydrogen bonds : angle 4.72549 / 3.33 ( 1449) link_ALPHA1-2 : bond 0.00165 / 0.08 ( 3) link_ALPHA1-2 : angle 1.89461 / 1.02 ( 9) link_ALPHA1-3 : bond 0.01596 / 0.79 ( 6) link_ALPHA1-3 : angle 2.92151 / 1.91 ( 18) link_ALPHA1-6 : bond 0.00547 / 0.26 ( 6) link_ALPHA1-6 : angle 1.43306 / 0.84 ( 18) link_BETA1-4 : bond 0.00528 / 0.34 ( 36) link_BETA1-4 : angle 2.15133 / 1.46 ( 108) link_BETA1-6 : bond 0.00162 / 0.07 ( 3) link_BETA1-6 : angle 1.68491 / 0.86 ( 9) link_NAG-ASN : bond 0.00268 / 0.18 ( 33) link_NAG-ASN : angle 2.01090 / 1.24 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3582.10 seconds wall clock time: 62 minutes 31.80 seconds (3751.80 seconds total)