Starting phenix.real_space_refine on Sat Aug 23 23:12:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejh_28182/08_2025/8ejh_28182.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejh_28182/08_2025/8ejh_28182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ejh_28182/08_2025/8ejh_28182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejh_28182/08_2025/8ejh_28182.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ejh_28182/08_2025/8ejh_28182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejh_28182/08_2025/8ejh_28182.map" } resolution = 3.71 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= 0.033 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 105 5.16 5 C 9492 2.51 5 N 2418 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15186 Number of models: 1 Model: "" Number of chains: 45 Chain: "C" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1522 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1522 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "c" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "A" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1522 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "b" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "a" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1339 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 943 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 943 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "h" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 943 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "l" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "h" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.00, per 1000 atoms: 0.20 Number of scatterers: 15186 At special positions: 0 Unit cell: (135.7, 148.35, 121.9, 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 105 16.00 O 3171 8.00 N 2418 7.00 C 9492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 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=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.04 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.02 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.04 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.02 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.02 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.06 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.08 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.06 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 104 " distance=2.08 Simple disulfide: pdb=" SG CYS h 23 " - pdb=" SG CYS h 104 " distance=2.06 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 104 " distance=2.08 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 V 4 " - " MAN V 5 " " MAN i 4 " - " MAN i 5 " " MAN k 4 " - " MAN k 5 " ALPHA1-3 " BMA E 3 " - " MAN J 201 " " MAN E 4 " - " MAN E 5 " " BMA P 3 " - " MAN h 201 " " MAN P 4 " - " MAN P 5 " " BMA V 3 " - " MAN V 4 " " MAN V 6 " - " MAN V 7 " " BMA Y 3 " - " MAN H 201 " " MAN Y 4 " - " MAN Y 5 " " BMA i 3 " - " MAN i 4 " " MAN i 6 " - " MAN i 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 6 " " BMA Y 3 " - " MAN Y 4 " " BMA i 3 " - " MAN i 6 " " BMA k 3 " - " MAN k 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG 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 i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG D 1 " - " ASN C 79 " " NAG E 1 " - " ASN C 89 " " NAG F 1 " - " ASN C 99 " " NAG G 1 " - " ASN C 109 " " NAG I 1 " - " ASN C 119 " " NAG M 1 " - " ASN C 167 " " NAG N 1 " - " ASN C 224 " " NAG O 1 " - " ASN B 79 " " NAG P 1 " - " ASN B 89 " " NAG Q 1 " - " ASN B 99 " " NAG R 1 " - " ASN B 109 " " NAG S 1 " - " ASN B 119 " " NAG T 1 " - " ASN B 167 " " NAG U 1 " - " ASN B 224 " " NAG V 1 " - " ASN c 365 " " NAG W 1 " - " ASN c 373 " " NAG X 1 " - " ASN A 79 " " NAG Y 1 " - " ASN A 89 " " NAG Z 1 " - " ASN A 99 " " NAG a 701 " - " ASN a 390 " " NAG a 702 " - " ASN a 395 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " " NAG d 1 " - " ASN A 109 " " NAG e 1 " - " ASN A 119 " " NAG f 1 " - " ASN A 167 " " NAG g 1 " - " ASN A 224 " " NAG i 1 " - " ASN b 365 " " NAG j 1 " - " ASN b 373 " " NAG k 1 " - " ASN a 365 " " NAG m 1 " - " ASN a 373 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 449.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3270 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 30 sheets defined 26.9% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 76 through 81 removed outlier: 4.292A pdb=" N MET C 80 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 130 through 143 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 Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 76 through 81 removed outlier: 4.293A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 130 through 143 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 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'c' and resid 294 through 301 removed outlier: 4.146A pdb=" N CYS c 301 " --> pdb=" O ALA c 297 " (cutoff:3.500A) Processing helix chain 'c' and resid 302 through 304 No H-bonds generated for 'chain 'c' and resid 302 through 304' Processing helix chain 'c' and resid 308 through 326 removed outlier: 3.707A pdb=" N LEU c 326 " --> pdb=" O ALA c 322 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 339 Processing helix chain 'c' and resid 340 through 345 Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.969A 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 424 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 76 through 81 removed outlier: 4.292A pdb=" N MET A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 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 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'b' and resid 294 through 301 removed outlier: 4.146A pdb=" N CYS b 301 " --> pdb=" O ALA b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 302 through 304 No H-bonds generated for 'chain 'b' and resid 302 through 304' Processing helix chain 'b' and resid 308 through 326 removed outlier: 3.707A pdb=" N LEU b 326 " --> pdb=" O ALA b 322 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 339 Processing helix chain 'b' and resid 340 through 345 Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.969A 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 424 Processing helix chain 'a' and resid 294 through 301 removed outlier: 4.146A pdb=" N CYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) Processing helix chain 'a' and resid 302 through 304 No H-bonds generated for 'chain 'a' and resid 302 through 304' Processing helix chain 'a' and resid 308 through 326 removed outlier: 3.707A pdb=" N LEU a 326 " --> pdb=" O ALA a 322 " (cutoff:3.500A) Processing helix chain 'a' and resid 334 through 339 Processing helix chain 'a' and resid 340 through 345 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.969A 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 424 Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.920A pdb=" N PHE H 37 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'J' and resid 29 through 37 removed outlier: 3.920A pdb=" N PHE J 37 " --> pdb=" O PHE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 72 Processing helix chain 'J' and resid 82 through 84 No H-bonds generated for 'chain 'J' and resid 82 through 84' Processing helix chain 'K' and resid 95 through 99 Processing helix chain 'h' and resid 29 through 37 removed outlier: 3.920A pdb=" N PHE h 37 " --> pdb=" O PHE h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 69 through 72 Processing helix chain 'h' and resid 82 through 84 No H-bonds generated for 'chain 'h' and resid 82 through 84' Processing helix chain 'l' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 72 Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 88 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 88 Processing sheet with id=AA5, first strand: chain 'c' and resid 279 through 280 Processing sheet with id=AA6, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AA7, first strand: chain 'A' and resid 66 through 72 Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 88 Processing sheet with id=AA9, first strand: chain 'b' and resid 279 through 280 Processing sheet with id=AB1, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'a' and resid 279 through 280 Processing sheet with id=AB3, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.528A pdb=" N SER H 79 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS H 104 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP H 118 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG H 106 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.022A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AC1, first strand: chain 'J' and resid 7 through 9 removed outlier: 3.528A pdb=" N SER J 79 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP J 52 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG J 43 " --> pdb=" O TRP J 52 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS J 104 " --> pdb=" O TRP J 118 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP J 118 " --> pdb=" O CYS J 104 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG J 106 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP J 52 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG J 43 " --> pdb=" O TRP J 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AC5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.022A pdb=" N GLN K 43 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU K 52 " --> pdb=" O GLN K 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AC7, first strand: chain 'h' and resid 7 through 9 removed outlier: 3.528A pdb=" N SER h 79 " --> pdb=" O SER h 88 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP h 52 " --> pdb=" O ARG h 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG h 43 " --> pdb=" O TRP h 52 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N CYS h 104 " --> pdb=" O TRP h 118 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP h 118 " --> pdb=" O CYS h 104 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG h 106 " --> pdb=" O ASP h 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 65 through 67 removed outlier: 5.348A pdb=" N TRP h 52 " --> pdb=" O ARG h 43 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG h 43 " --> pdb=" O TRP h 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'l' and resid 4 through 5 Processing sheet with id=AD2, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.022A pdb=" N GLN l 43 " --> pdb=" O LEU l 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU l 52 " --> pdb=" O GLN l 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 10 through 12 606 hydrogen bonds defined for protein. 1566 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: 2.33 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2736 1.32 - 1.46: 5318 1.46 - 1.59: 7267 1.59 - 1.73: 42 1.73 - 1.87: 153 Bond restraints: 15516 Sorted by residual: bond pdb=" CB HIS K 44 " pdb=" CG HIS K 44 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.41e+01 bond pdb=" CB HIS L 44 " pdb=" CG HIS L 44 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.40e+01 bond pdb=" CB HIS l 44 " pdb=" CG HIS l 44 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.39e+01 bond pdb=" CB HIS L 106 " pdb=" CG HIS L 106 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.06e+01 bond pdb=" CB HIS l 106 " pdb=" CG HIS l 106 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.03e+01 ... (remaining 15511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16497 2.01 - 4.02: 3590 4.02 - 6.02: 778 6.02 - 8.03: 126 8.03 - 10.04: 48 Bond angle restraints: 21039 Sorted by residual: angle pdb=" N ASP c 311 " pdb=" CA ASP c 311 " pdb=" C ASP c 311 " ideal model delta sigma weight residual 111.69 101.98 9.71 1.23e+00 6.61e-01 6.24e+01 angle pdb=" N ASP a 311 " pdb=" CA ASP a 311 " pdb=" C ASP a 311 " ideal model delta sigma weight residual 111.69 102.01 9.68 1.23e+00 6.61e-01 6.20e+01 angle pdb=" N ASP b 311 " pdb=" CA ASP b 311 " pdb=" C ASP b 311 " ideal model delta sigma weight residual 111.69 102.01 9.68 1.23e+00 6.61e-01 6.19e+01 angle pdb=" C GLN h 44 " pdb=" N PRO h 45 " pdb=" CA PRO h 45 " ideal model delta sigma weight residual 119.66 124.99 -5.33 7.30e-01 1.88e+00 5.32e+01 angle pdb=" C GLN J 44 " pdb=" N PRO J 45 " pdb=" CA PRO J 45 " ideal model delta sigma weight residual 119.66 124.98 -5.32 7.30e-01 1.88e+00 5.30e+01 ... (remaining 21034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 9943 21.81 - 43.62: 275 43.62 - 65.43: 51 65.43 - 87.24: 111 87.24 - 109.05: 78 Dihedral angle restraints: 10458 sinusoidal: 5352 harmonic: 5106 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 104 " pdb=" CB CYS K 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.20 -62.20 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS l 23 " pdb=" SG CYS l 23 " pdb=" SG CYS l 104 " pdb=" CB CYS l 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.20 -62.20 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 104 " pdb=" CB CYS L 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.19 -62.19 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 10455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1641 0.101 - 0.202: 564 0.202 - 0.302: 236 0.302 - 0.403: 103 0.403 - 0.504: 60 Chirality restraints: 2604 Sorted by residual: chirality pdb=" C1 MAN V 6 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 6 " pdb=" O5 MAN V 6 " both_signs ideal model delta sigma weight residual False 2.40 2.13 0.27 2.00e-02 2.50e+03 1.89e+02 chirality pdb=" C1 MAN i 6 " pdb=" O6 BMA i 3 " pdb=" C2 MAN i 6 " pdb=" O5 MAN i 6 " both_signs ideal model delta sigma weight residual False 2.40 2.13 0.27 2.00e-02 2.50e+03 1.87e+02 chirality pdb=" C1 MAN k 6 " pdb=" O6 BMA k 3 " pdb=" C2 MAN k 6 " pdb=" O5 MAN k 6 " both_signs ideal model delta sigma weight residual False 2.40 2.13 0.27 2.00e-02 2.50e+03 1.86e+02 ... (remaining 2601 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " -0.238 2.00e-02 2.50e+03 1.93e-01 4.68e+02 pdb=" C7 NAG Y 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 1 " -0.238 2.00e-02 2.50e+03 1.93e-01 4.68e+02 pdb=" C7 NAG P 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG P 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG P 1 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG P 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.238 2.00e-02 2.50e+03 1.93e-01 4.68e+02 pdb=" C7 NAG E 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.030 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4647 2.84 - 3.35: 13654 3.35 - 3.87: 25437 3.87 - 4.38: 29641 4.38 - 4.90: 47957 Nonbonded interactions: 121336 Sorted by model distance: nonbonded pdb=" O4 MAN P 4 " pdb=" O6 MAN P 4 " model vdw 2.321 3.040 nonbonded pdb=" O4 MAN E 4 " pdb=" O6 MAN E 4 " model vdw 2.321 3.040 nonbonded pdb=" O4 MAN Y 4 " pdb=" O6 MAN Y 4 " model vdw 2.321 3.040 nonbonded pdb=" O4 MAN k 4 " pdb=" O6 MAN k 4 " model vdw 2.380 3.040 nonbonded pdb=" O4 MAN i 4 " pdb=" O6 MAN i 4 " model vdw 2.380 3.040 ... (remaining 121331 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'd' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'Q' selection = chain 'S' selection = chain 'W' selection = chain 'Z' selection = chain 'e' selection = chain 'j' selection = chain 'm' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'h' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'V' selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.720 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.117 15642 Z= 1.158 Angle : 1.906 13.568 21390 Z= 1.167 Chirality : 0.146 0.504 2604 Planarity : 0.011 0.193 2514 Dihedral : 17.279 109.053 7107 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.18 (0.20), residues: 1731 helix: -0.37 (0.25), residues: 372 sheet: 0.26 (0.26), residues: 375 loop : -0.05 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG h 75 TYR 0.048 0.007 TYR B 253 PHE 0.027 0.006 PHE l 99 TRP 0.075 0.010 TRP H 52 HIS 0.006 0.002 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.02127 (15516) covalent geometry : angle 1.82534 (21039) SS BOND : bond 0.02120 ( 27) SS BOND : angle 3.70606 ( 54) hydrogen bonds : bond 0.18297 ( 552) hydrogen bonds : angle 7.48017 ( 1566) link_ALPHA1-2 : bond 0.08703 ( 3) link_ALPHA1-2 : angle 5.58010 ( 9) link_ALPHA1-3 : bond 0.07270 ( 12) link_ALPHA1-3 : angle 6.47357 ( 36) link_ALPHA1-6 : bond 0.04013 ( 6) link_ALPHA1-6 : angle 2.04702 ( 18) link_BETA1-4 : bond 0.07223 ( 45) link_BETA1-4 : angle 5.48432 ( 135) link_NAG-ASN : bond 0.07388 ( 33) link_NAG-ASN : angle 3.11118 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 MET cc_start: 0.8364 (mmm) cc_final: 0.7641 (mmm) REVERT: C 194 MET cc_start: 0.8339 (tpp) cc_final: 0.7888 (tpp) REVERT: B 80 MET cc_start: 0.8297 (mmm) cc_final: 0.7500 (mmt) REVERT: B 194 MET cc_start: 0.8366 (tpp) cc_final: 0.8139 (tpp) REVERT: A 80 MET cc_start: 0.8351 (mmm) cc_final: 0.7756 (mmt) REVERT: A 194 MET cc_start: 0.8278 (tpp) cc_final: 0.7907 (ttm) REVERT: H 13 LEU cc_start: 0.8014 (mt) cc_final: 0.7703 (pp) REVERT: H 52 TRP cc_start: 0.8554 (t60) cc_final: 0.8283 (t60) REVERT: H 56 ILE cc_start: 0.9329 (tt) cc_final: 0.9052 (tt) REVERT: H 68 ASN cc_start: 0.8838 (t0) cc_final: 0.8399 (t0) REVERT: H 80 VAL cc_start: 0.8784 (p) cc_final: 0.8571 (t) REVERT: H 98 ASP cc_start: 0.8127 (m-30) cc_final: 0.7785 (m-30) REVERT: L 3 THR cc_start: 0.9317 (p) cc_final: 0.8990 (p) REVERT: L 5 THR cc_start: 0.8172 (m) cc_final: 0.7895 (p) REVERT: L 18 ARG cc_start: 0.8162 (ttm170) cc_final: 0.7704 (ttp80) REVERT: L 90 THR cc_start: 0.8425 (m) cc_final: 0.8115 (p) REVERT: L 99 PHE cc_start: 0.6940 (m-80) cc_final: 0.6723 (m-80) REVERT: J 52 TRP cc_start: 0.8638 (t60) cc_final: 0.8388 (t60) REVERT: J 87 PHE cc_start: 0.8165 (p90) cc_final: 0.7903 (p90) REVERT: J 98 ASP cc_start: 0.7786 (m-30) cc_final: 0.7563 (m-30) REVERT: J 122 THR cc_start: 0.7888 (m) cc_final: 0.7672 (p) REVERT: K 5 THR cc_start: 0.8308 (m) cc_final: 0.8083 (p) REVERT: K 90 THR cc_start: 0.8444 (m) cc_final: 0.8235 (p) REVERT: K 99 PHE cc_start: 0.6802 (m-80) cc_final: 0.6418 (m-80) REVERT: h 13 LEU cc_start: 0.7856 (mt) cc_final: 0.7512 (pp) REVERT: h 87 PHE cc_start: 0.8310 (p90) cc_final: 0.8095 (p90) REVERT: l 18 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7699 (ttp80) REVERT: l 90 THR cc_start: 0.8466 (m) cc_final: 0.8188 (p) REVERT: l 99 PHE cc_start: 0.6714 (m-80) cc_final: 0.6325 (m-80) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.1235 time to fit residues: 93.0664 Evaluate side-chains 283 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 302 ASN b 302 ASN a 302 ASN a 416 GLN L 105 GLN L 106 HIS K 6 GLN K 105 GLN l 6 GLN l 105 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.109329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084824 restraints weight = 36850.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088363 restraints weight = 19679.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.090730 restraints weight = 13682.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.092211 restraints weight = 10903.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093341 restraints weight = 9475.631| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15642 Z= 0.199 Angle : 0.922 9.425 21390 Z= 0.440 Chirality : 0.050 0.283 2604 Planarity : 0.005 0.037 2514 Dihedral : 14.035 73.246 3903 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.95 % Allowed : 10.07 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.10 (0.20), residues: 1731 helix: 0.37 (0.28), residues: 378 sheet: 0.28 (0.25), residues: 405 loop : -0.33 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 325 TYR 0.024 0.002 TYR J 112C PHE 0.022 0.002 PHE H 30 TRP 0.038 0.002 TRP h 52 HIS 0.009 0.002 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00418 (15516) covalent geometry : angle 0.84167 (21039) SS BOND : bond 0.00566 ( 27) SS BOND : angle 1.46807 ( 54) hydrogen bonds : bond 0.05385 ( 552) hydrogen bonds : angle 5.63714 ( 1566) link_ALPHA1-2 : bond 0.00522 ( 3) link_ALPHA1-2 : angle 2.44901 ( 9) link_ALPHA1-3 : bond 0.02234 ( 12) link_ALPHA1-3 : angle 3.85381 ( 36) link_ALPHA1-6 : bond 0.00710 ( 6) link_ALPHA1-6 : angle 1.56085 ( 18) link_BETA1-4 : bond 0.01069 ( 45) link_BETA1-4 : angle 3.79121 ( 135) link_NAG-ASN : bond 0.00600 ( 33) link_NAG-ASN : angle 2.47604 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 359 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8147 (ttpp) REVERT: B 116 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8576 (mmmt) REVERT: B 156 ASP cc_start: 0.7671 (t70) cc_final: 0.6913 (t0) REVERT: B 161 LYS cc_start: 0.8439 (ttmt) cc_final: 0.7887 (ttpp) REVERT: B 194 MET cc_start: 0.9150 (tpp) cc_final: 0.8945 (tpp) REVERT: c 282 ARG cc_start: 0.8446 (tpt90) cc_final: 0.7851 (tpm170) REVERT: c 303 GLU cc_start: 0.6151 (tp30) cc_final: 0.5401 (tp30) REVERT: c 332 MET cc_start: 0.7647 (mmp) cc_final: 0.7446 (mmm) REVERT: c 351 MET cc_start: 0.8835 (tpp) cc_final: 0.8583 (tpp) REVERT: c 420 MET cc_start: 0.7259 (mmt) cc_final: 0.6633 (tpt) REVERT: A 96 MET cc_start: 0.7737 (mmm) cc_final: 0.7400 (mmm) REVERT: A 116 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8440 (mmmt) REVERT: A 134 MET cc_start: 0.9421 (tpp) cc_final: 0.9080 (tpp) REVERT: A 161 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8008 (tptt) REVERT: b 284 MET cc_start: 0.8195 (mtm) cc_final: 0.7593 (mtm) REVERT: b 303 GLU cc_start: 0.6219 (tp30) cc_final: 0.5557 (tp30) REVERT: b 305 HIS cc_start: 0.7373 (m90) cc_final: 0.6835 (m-70) REVERT: b 332 MET cc_start: 0.7570 (mmp) cc_final: 0.7348 (mmm) REVERT: b 420 MET cc_start: 0.7311 (mmt) cc_final: 0.6868 (tpt) REVERT: b 423 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7798 (mp10) REVERT: a 284 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7936 (mtp) REVERT: a 306 ASP cc_start: 0.8397 (p0) cc_final: 0.8111 (p0) REVERT: a 326 LEU cc_start: 0.7970 (mt) cc_final: 0.7577 (mt) REVERT: a 359 MET cc_start: 0.9018 (mtt) cc_final: 0.8772 (mtm) REVERT: a 409 ASN cc_start: 0.8812 (m-40) cc_final: 0.8396 (m110) REVERT: a 420 MET cc_start: 0.7460 (mmt) cc_final: 0.6949 (tpt) REVERT: H 6 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6345 (mm-30) REVERT: H 13 LEU cc_start: 0.7313 (mt) cc_final: 0.7068 (pp) REVERT: H 53 ILE cc_start: 0.8085 (mt) cc_final: 0.7782 (mt) REVERT: H 98 ASP cc_start: 0.7293 (m-30) cc_final: 0.6834 (m-30) REVERT: H 112 TYR cc_start: 0.7952 (p90) cc_final: 0.7142 (p90) REVERT: L 17 GLU cc_start: 0.6839 (mp0) cc_final: 0.6560 (mp0) REVERT: L 18 ARG cc_start: 0.8358 (ttm170) cc_final: 0.7694 (ttp80) REVERT: L 90 THR cc_start: 0.8202 (m) cc_final: 0.7806 (p) REVERT: L 94 LEU cc_start: 0.7910 (tp) cc_final: 0.7267 (tt) REVERT: L 99 PHE cc_start: 0.6814 (m-80) cc_final: 0.5721 (m-80) REVERT: L 125 GLU cc_start: 0.6717 (tt0) cc_final: 0.6366 (tt0) REVERT: J 5 GLN cc_start: 0.7028 (tp40) cc_final: 0.6579 (tp-100) REVERT: J 43 ARG cc_start: 0.8054 (ttp-170) cc_final: 0.7733 (ttp-170) REVERT: J 52 TRP cc_start: 0.7619 (t60) cc_final: 0.7401 (t60) REVERT: J 87 PHE cc_start: 0.8446 (p90) cc_final: 0.8193 (p90) REVERT: J 98 ASP cc_start: 0.7004 (m-30) cc_final: 0.6519 (m-30) REVERT: K 5 THR cc_start: 0.7905 (m) cc_final: 0.7687 (p) REVERT: K 18 ARG cc_start: 0.8424 (ttm170) cc_final: 0.7750 (ttp80) REVERT: K 90 THR cc_start: 0.8112 (m) cc_final: 0.7814 (p) REVERT: K 94 LEU cc_start: 0.7876 (tp) cc_final: 0.7419 (tt) REVERT: K 99 PHE cc_start: 0.7044 (m-80) cc_final: 0.6489 (m-80) REVERT: h 43 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7993 (mtm110) REVERT: h 53 ILE cc_start: 0.8114 (mt) cc_final: 0.7555 (mt) REVERT: h 78 ILE cc_start: 0.8357 (mt) cc_final: 0.7790 (tp) REVERT: h 87 PHE cc_start: 0.8435 (p90) cc_final: 0.8037 (p90) REVERT: h 112 TYR cc_start: 0.8145 (p90) cc_final: 0.7805 (p90) REVERT: l 17 GLU cc_start: 0.7446 (mp0) cc_final: 0.7008 (mp0) REVERT: l 18 ARG cc_start: 0.8610 (ttm170) cc_final: 0.7775 (ttp80) REVERT: l 90 THR cc_start: 0.8181 (m) cc_final: 0.7783 (p) REVERT: l 99 PHE cc_start: 0.7015 (m-80) cc_final: 0.6206 (m-80) REVERT: l 125 GLU cc_start: 0.6042 (tt0) cc_final: 0.5634 (tt0) outliers start: 30 outliers final: 19 residues processed: 371 average time/residue: 0.1199 time to fit residues: 64.5459 Evaluate side-chains 312 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 292 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain a residue 273 ASP Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 68 optimal weight: 0.8980 chunk 141 optimal weight: 0.0670 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 HIS C 158 ASN C 170 HIS B 92 HIS B 170 HIS c 423 GLN ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS J 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.106717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083247 restraints weight = 36775.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086757 restraints weight = 18805.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089131 restraints weight = 12797.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090694 restraints weight = 10043.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.091676 restraints weight = 8576.380| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15642 Z= 0.169 Angle : 0.816 12.436 21390 Z= 0.382 Chirality : 0.046 0.241 2604 Planarity : 0.004 0.038 2514 Dihedral : 10.706 62.921 3903 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.18 % Allowed : 11.18 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.16 (0.20), residues: 1731 helix: 0.67 (0.28), residues: 375 sheet: 0.31 (0.25), residues: 420 loop : -0.57 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 67 TYR 0.029 0.002 TYR a 419 PHE 0.026 0.002 PHE h 30 TRP 0.031 0.002 TRP H 52 HIS 0.007 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00361 (15516) covalent geometry : angle 0.74641 (21039) SS BOND : bond 0.00519 ( 27) SS BOND : angle 1.92240 ( 54) hydrogen bonds : bond 0.04534 ( 552) hydrogen bonds : angle 5.35715 ( 1566) link_ALPHA1-2 : bond 0.00242 ( 3) link_ALPHA1-2 : angle 1.92699 ( 9) link_ALPHA1-3 : bond 0.01930 ( 12) link_ALPHA1-3 : angle 3.54743 ( 36) link_ALPHA1-6 : bond 0.00614 ( 6) link_ALPHA1-6 : angle 1.65576 ( 18) link_BETA1-4 : bond 0.01027 ( 45) link_BETA1-4 : angle 3.18045 ( 135) link_NAG-ASN : bond 0.00450 ( 33) link_NAG-ASN : angle 2.08136 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 315 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 156 ASP cc_start: 0.7521 (t70) cc_final: 0.6767 (t0) REVERT: C 161 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8217 (ttpp) REVERT: C 194 MET cc_start: 0.8894 (tpp) cc_final: 0.8561 (ttp) REVERT: B 116 LYS cc_start: 0.9006 (mmtm) cc_final: 0.8726 (mmmt) REVERT: B 156 ASP cc_start: 0.7823 (t70) cc_final: 0.7592 (t0) REVERT: B 161 LYS cc_start: 0.8489 (ttmt) cc_final: 0.7761 (tptt) REVERT: c 282 ARG cc_start: 0.8484 (tpt90) cc_final: 0.7932 (tpm170) REVERT: c 303 GLU cc_start: 0.5985 (tp30) cc_final: 0.5569 (tp30) REVERT: c 326 LEU cc_start: 0.8042 (mp) cc_final: 0.7504 (tp) REVERT: c 351 MET cc_start: 0.8868 (tpp) cc_final: 0.8603 (tpp) REVERT: c 419 TYR cc_start: 0.6989 (t80) cc_final: 0.6252 (t80) REVERT: c 420 MET cc_start: 0.7688 (mmt) cc_final: 0.6693 (tpt) REVERT: A 116 LYS cc_start: 0.8931 (mmtm) cc_final: 0.8633 (mmmt) REVERT: A 156 ASP cc_start: 0.8094 (p0) cc_final: 0.7793 (p0) REVERT: A 161 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8029 (tptt) REVERT: b 284 MET cc_start: 0.8156 (mtm) cc_final: 0.7695 (mtm) REVERT: b 303 GLU cc_start: 0.6427 (tp30) cc_final: 0.6227 (tp30) REVERT: b 418 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8457 (mt-10) REVERT: b 419 TYR cc_start: 0.6669 (t80) cc_final: 0.6077 (t80) REVERT: b 420 MET cc_start: 0.7764 (mmt) cc_final: 0.7030 (tpt) REVERT: a 284 MET cc_start: 0.8439 (mtp) cc_final: 0.8030 (mtp) REVERT: a 303 GLU cc_start: 0.6210 (tp30) cc_final: 0.5915 (tp30) REVERT: a 348 GLN cc_start: 0.5011 (mt0) cc_final: 0.4222 (tt0) REVERT: a 420 MET cc_start: 0.7914 (mmt) cc_final: 0.7283 (tpt) REVERT: H 43 ARG cc_start: 0.8538 (ttp-170) cc_final: 0.8176 (ttp80) REVERT: H 53 ILE cc_start: 0.8294 (mt) cc_final: 0.7913 (mt) REVERT: H 98 ASP cc_start: 0.7437 (m-30) cc_final: 0.7012 (m-30) REVERT: H 110 TYR cc_start: 0.8300 (t80) cc_final: 0.7949 (t80) REVERT: H 112 TYR cc_start: 0.8054 (p90) cc_final: 0.7185 (p90) REVERT: L 17 GLU cc_start: 0.7127 (mp0) cc_final: 0.6826 (mp0) REVERT: L 18 ARG cc_start: 0.8432 (ttm170) cc_final: 0.7772 (ttp80) REVERT: L 90 THR cc_start: 0.8303 (m) cc_final: 0.7979 (p) REVERT: L 94 LEU cc_start: 0.7744 (tp) cc_final: 0.7053 (tt) REVERT: L 99 PHE cc_start: 0.7307 (m-80) cc_final: 0.6352 (m-80) REVERT: L 122 THR cc_start: 0.7898 (p) cc_final: 0.7632 (p) REVERT: J 5 GLN cc_start: 0.7203 (tp40) cc_final: 0.6734 (tp-100) REVERT: J 52 TRP cc_start: 0.7913 (t60) cc_final: 0.7370 (t60) REVERT: J 87 PHE cc_start: 0.8326 (p90) cc_final: 0.7963 (p90) REVERT: J 98 ASP cc_start: 0.7052 (m-30) cc_final: 0.6645 (m-30) REVERT: K 5 THR cc_start: 0.7846 (m) cc_final: 0.7640 (p) REVERT: K 17 GLU cc_start: 0.7510 (mp0) cc_final: 0.7164 (mp0) REVERT: K 90 THR cc_start: 0.8288 (m) cc_final: 0.7975 (p) REVERT: K 94 LEU cc_start: 0.7724 (tp) cc_final: 0.7436 (tt) REVERT: K 99 PHE cc_start: 0.7521 (m-80) cc_final: 0.6984 (m-80) REVERT: h 43 ARG cc_start: 0.8214 (ttp80) cc_final: 0.8001 (mtm110) REVERT: h 52 TRP cc_start: 0.7891 (t60) cc_final: 0.7590 (t60) REVERT: h 53 ILE cc_start: 0.8157 (mt) cc_final: 0.7642 (mt) REVERT: l 17 GLU cc_start: 0.7675 (mp0) cc_final: 0.7347 (mp0) REVERT: l 18 ARG cc_start: 0.8263 (ttm170) cc_final: 0.7793 (ttp80) REVERT: l 90 THR cc_start: 0.8302 (m) cc_final: 0.7896 (p) REVERT: l 94 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7712 (tt) REVERT: l 99 PHE cc_start: 0.7244 (m-80) cc_final: 0.6465 (m-80) REVERT: l 125 GLU cc_start: 0.6335 (tt0) cc_final: 0.5898 (tt0) outliers start: 49 outliers final: 28 residues processed: 338 average time/residue: 0.1149 time to fit residues: 57.2958 Evaluate side-chains 307 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 278 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain l residue 39 LEU Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 107 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 0.0970 chunk 156 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN B 69 GLN H 113 HIS K 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.105140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080876 restraints weight = 37871.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084224 restraints weight = 20077.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086470 restraints weight = 14062.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087949 restraints weight = 11270.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088831 restraints weight = 9782.686| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15642 Z= 0.199 Angle : 0.801 11.198 21390 Z= 0.374 Chirality : 0.046 0.261 2604 Planarity : 0.004 0.034 2514 Dihedral : 8.266 50.692 3903 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.83 % Allowed : 12.48 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.21 (0.20), residues: 1731 helix: 0.87 (0.28), residues: 375 sheet: 0.27 (0.25), residues: 417 loop : -0.71 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 379 TYR 0.026 0.002 TYR a 419 PHE 0.014 0.002 PHE L 76 TRP 0.052 0.002 TRP H 52 HIS 0.006 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00448 (15516) covalent geometry : angle 0.74215 (21039) SS BOND : bond 0.00753 ( 27) SS BOND : angle 2.09150 ( 54) hydrogen bonds : bond 0.04220 ( 552) hydrogen bonds : angle 5.30044 ( 1566) link_ALPHA1-2 : bond 0.00045 ( 3) link_ALPHA1-2 : angle 1.90347 ( 9) link_ALPHA1-3 : bond 0.01904 ( 12) link_ALPHA1-3 : angle 3.29015 ( 36) link_ALPHA1-6 : bond 0.00734 ( 6) link_ALPHA1-6 : angle 1.75972 ( 18) link_BETA1-4 : bond 0.00793 ( 45) link_BETA1-4 : angle 2.81556 ( 135) link_NAG-ASN : bond 0.00348 ( 33) link_NAG-ASN : angle 1.91370 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 305 time to evaluate : 0.532 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: C 72 GLU cc_start: 0.7538 (pm20) cc_final: 0.7333 (pm20) REVERT: C 156 ASP cc_start: 0.8076 (t70) cc_final: 0.7000 (t0) REVERT: C 161 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8254 (ttpp) REVERT: C 194 MET cc_start: 0.8918 (tpp) cc_final: 0.8475 (tpp) REVERT: B 116 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8824 (mmmt) REVERT: B 156 ASP cc_start: 0.8013 (t70) cc_final: 0.7529 (t0) REVERT: B 161 LYS cc_start: 0.8578 (ttmt) cc_final: 0.7923 (tptt) REVERT: c 282 ARG cc_start: 0.8506 (tpt90) cc_final: 0.7963 (tpm170) REVERT: c 303 GLU cc_start: 0.6438 (tp30) cc_final: 0.5897 (tp30) REVERT: c 351 MET cc_start: 0.8911 (tpp) cc_final: 0.8617 (tpp) REVERT: c 419 TYR cc_start: 0.6936 (t80) cc_final: 0.6495 (t80) REVERT: c 420 MET cc_start: 0.7615 (mmt) cc_final: 0.6680 (tpt) REVERT: A 80 MET cc_start: 0.8814 (mmt) cc_final: 0.8078 (mmm) REVERT: A 116 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8794 (mmmt) REVERT: A 156 ASP cc_start: 0.8034 (p0) cc_final: 0.7775 (p0) REVERT: A 161 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8428 (ttpp) REVERT: A 194 MET cc_start: 0.8717 (tpp) cc_final: 0.8143 (ttm) REVERT: b 284 MET cc_start: 0.8183 (mtm) cc_final: 0.7650 (mtm) REVERT: b 420 MET cc_start: 0.7739 (mmt) cc_final: 0.7153 (tpt) REVERT: a 284 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7959 (mtp) REVERT: a 303 GLU cc_start: 0.6642 (tp30) cc_final: 0.6183 (tp30) REVERT: a 311 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7687 (t0) REVERT: a 326 LEU cc_start: 0.8027 (mt) cc_final: 0.7291 (mt) REVERT: a 332 MET cc_start: 0.7715 (tpp) cc_final: 0.7495 (tpp) REVERT: a 348 GLN cc_start: 0.5157 (mt0) cc_final: 0.4356 (tt0) REVERT: a 420 MET cc_start: 0.7961 (mmt) cc_final: 0.7388 (tpt) REVERT: H 43 ARG cc_start: 0.8608 (ttp-170) cc_final: 0.8063 (mtm110) REVERT: H 53 ILE cc_start: 0.8347 (mt) cc_final: 0.7797 (mt) REVERT: H 90 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8191 (mtpt) REVERT: H 98 ASP cc_start: 0.7447 (m-30) cc_final: 0.7007 (m-30) REVERT: H 110 TYR cc_start: 0.8394 (t80) cc_final: 0.8147 (t80) REVERT: H 112 TYR cc_start: 0.8180 (p90) cc_final: 0.7330 (p90) REVERT: L 17 GLU cc_start: 0.7248 (mp0) cc_final: 0.6946 (mp0) REVERT: L 18 ARG cc_start: 0.8404 (ttm170) cc_final: 0.7592 (ttp80) REVERT: L 66 LYS cc_start: 0.6522 (mptt) cc_final: 0.6322 (mmtm) REVERT: L 90 THR cc_start: 0.8400 (m) cc_final: 0.8143 (p) REVERT: L 94 LEU cc_start: 0.7822 (tp) cc_final: 0.7135 (tt) REVERT: L 99 PHE cc_start: 0.7212 (m-80) cc_final: 0.6395 (m-80) REVERT: J 5 GLN cc_start: 0.7207 (tp40) cc_final: 0.6768 (tp-100) REVERT: J 43 ARG cc_start: 0.8463 (ttp-170) cc_final: 0.8033 (mtm110) REVERT: J 52 TRP cc_start: 0.7937 (t60) cc_final: 0.7279 (t60) REVERT: J 87 PHE cc_start: 0.8309 (p90) cc_final: 0.7828 (p90) REVERT: J 98 ASP cc_start: 0.7141 (m-30) cc_final: 0.6629 (m-30) REVERT: K 5 THR cc_start: 0.7808 (m) cc_final: 0.7536 (p) REVERT: K 17 GLU cc_start: 0.7730 (mp0) cc_final: 0.6821 (mp0) REVERT: K 90 THR cc_start: 0.8630 (m) cc_final: 0.8358 (p) REVERT: K 94 LEU cc_start: 0.7693 (tp) cc_final: 0.7263 (tt) REVERT: K 99 PHE cc_start: 0.7533 (m-80) cc_final: 0.7008 (m-80) REVERT: h 43 ARG cc_start: 0.8311 (ttp80) cc_final: 0.7996 (mtm110) REVERT: h 52 TRP cc_start: 0.8038 (t60) cc_final: 0.7592 (t60) REVERT: h 53 ILE cc_start: 0.8258 (mt) cc_final: 0.7628 (mt) REVERT: h 87 PHE cc_start: 0.8292 (p90) cc_final: 0.7998 (p90) REVERT: l 17 GLU cc_start: 0.7775 (mp0) cc_final: 0.7445 (mp0) REVERT: l 90 THR cc_start: 0.8526 (m) cc_final: 0.8165 (p) REVERT: l 94 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7564 (tt) REVERT: l 99 PHE cc_start: 0.7253 (m-80) cc_final: 0.6524 (m-80) outliers start: 59 outliers final: 36 residues processed: 335 average time/residue: 0.1107 time to fit residues: 54.9662 Evaluate side-chains 304 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 39 LEU Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 40 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 122 optimal weight: 0.0170 chunk 143 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN B 158 ASN A 149 GLN h 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.103777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.079596 restraints weight = 38251.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082946 restraints weight = 20235.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085172 restraints weight = 14126.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086645 restraints weight = 11329.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087523 restraints weight = 9815.844| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15642 Z= 0.210 Angle : 0.783 10.925 21390 Z= 0.369 Chirality : 0.045 0.267 2604 Planarity : 0.004 0.040 2514 Dihedral : 7.751 55.759 3903 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.72 % Favored : 94.11 % Rotamer: Outliers : 3.90 % Allowed : 13.45 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.34 (0.20), residues: 1731 helix: 0.93 (0.28), residues: 375 sheet: 0.24 (0.25), residues: 417 loop : -0.91 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 115 TYR 0.017 0.001 TYR a 419 PHE 0.017 0.002 PHE K 76 TRP 0.049 0.002 TRP H 52 HIS 0.005 0.001 HIS c 305 Details of bonding type rmsd covalent geometry : bond 0.00476 (15516) covalent geometry : angle 0.72422 (21039) SS BOND : bond 0.00687 ( 27) SS BOND : angle 2.22495 ( 54) hydrogen bonds : bond 0.04169 ( 552) hydrogen bonds : angle 5.27777 ( 1566) link_ALPHA1-2 : bond 0.00050 ( 3) link_ALPHA1-2 : angle 1.97283 ( 9) link_ALPHA1-3 : bond 0.01742 ( 12) link_ALPHA1-3 : angle 3.39555 ( 36) link_ALPHA1-6 : bond 0.00788 ( 6) link_ALPHA1-6 : angle 1.69488 ( 18) link_BETA1-4 : bond 0.00778 ( 45) link_BETA1-4 : angle 2.65937 ( 135) link_NAG-ASN : bond 0.00354 ( 33) link_NAG-ASN : angle 1.91159 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 283 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.9123 (mmtm) cc_final: 0.8824 (mmmt) REVERT: C 156 ASP cc_start: 0.8087 (t70) cc_final: 0.6999 (t0) REVERT: C 161 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8284 (ttpp) REVERT: C 194 MET cc_start: 0.8936 (tpp) cc_final: 0.8307 (ttp) REVERT: C 214 MET cc_start: 0.8069 (ptp) cc_final: 0.7741 (ptp) REVERT: B 116 LYS cc_start: 0.9148 (mmtm) cc_final: 0.8861 (mmmt) REVERT: B 161 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8004 (tptt) REVERT: c 282 ARG cc_start: 0.8529 (tpt90) cc_final: 0.7974 (tpm170) REVERT: c 311 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8012 (t0) REVERT: c 351 MET cc_start: 0.8964 (tpp) cc_final: 0.8666 (tpp) REVERT: c 419 TYR cc_start: 0.6936 (t80) cc_final: 0.6482 (t80) REVERT: c 420 MET cc_start: 0.7594 (mmt) cc_final: 0.6702 (tpt) REVERT: A 116 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8850 (mmmt) REVERT: A 161 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8431 (ttpp) REVERT: b 284 MET cc_start: 0.8209 (mtm) cc_final: 0.7715 (mtm) REVERT: b 332 MET cc_start: 0.7827 (tpp) cc_final: 0.7140 (tpp) REVERT: b 420 MET cc_start: 0.7774 (mmt) cc_final: 0.7503 (tpt) REVERT: a 282 ARG cc_start: 0.8514 (tpt90) cc_final: 0.8174 (tpm170) REVERT: a 284 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7980 (mtp) REVERT: a 303 GLU cc_start: 0.6774 (tp30) cc_final: 0.6404 (tp30) REVERT: a 311 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7361 (t0) REVERT: a 348 GLN cc_start: 0.5173 (mt0) cc_final: 0.4381 (tt0) REVERT: a 410 MET cc_start: 0.7875 (mtp) cc_final: 0.7528 (ttm) REVERT: a 420 MET cc_start: 0.7995 (mmt) cc_final: 0.7478 (tpt) REVERT: H 43 ARG cc_start: 0.8579 (ttp-170) cc_final: 0.8232 (mtm110) REVERT: H 53 ILE cc_start: 0.8428 (mt) cc_final: 0.7948 (mt) REVERT: H 90 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8229 (mtpt) REVERT: H 98 ASP cc_start: 0.7524 (m-30) cc_final: 0.7139 (m-30) REVERT: L 17 GLU cc_start: 0.7477 (mp0) cc_final: 0.7118 (mp0) REVERT: L 18 ARG cc_start: 0.8434 (ttm170) cc_final: 0.7565 (ttp80) REVERT: L 66 LYS cc_start: 0.6728 (mptt) cc_final: 0.6525 (mmtm) REVERT: L 90 THR cc_start: 0.8569 (m) cc_final: 0.8326 (p) REVERT: L 94 LEU cc_start: 0.7833 (tp) cc_final: 0.7165 (tt) REVERT: L 99 PHE cc_start: 0.7286 (m-80) cc_final: 0.6479 (m-80) REVERT: J 5 GLN cc_start: 0.7190 (tp40) cc_final: 0.6825 (tp-100) REVERT: J 43 ARG cc_start: 0.8439 (ttp-170) cc_final: 0.8089 (mtm110) REVERT: J 52 TRP cc_start: 0.7992 (t60) cc_final: 0.7307 (t60) REVERT: J 98 ASP cc_start: 0.7069 (m-30) cc_final: 0.6717 (m-30) REVERT: K 5 THR cc_start: 0.7739 (m) cc_final: 0.7527 (p) REVERT: K 17 GLU cc_start: 0.7901 (mp0) cc_final: 0.6922 (mp0) REVERT: K 90 THR cc_start: 0.8757 (m) cc_final: 0.8480 (p) REVERT: K 94 LEU cc_start: 0.7714 (tp) cc_final: 0.7269 (tt) REVERT: K 99 PHE cc_start: 0.7638 (m-80) cc_final: 0.7078 (m-80) REVERT: h 43 ARG cc_start: 0.8321 (ttp80) cc_final: 0.8004 (mtm110) REVERT: h 53 ILE cc_start: 0.8369 (mt) cc_final: 0.7836 (mt) REVERT: h 87 PHE cc_start: 0.8460 (p90) cc_final: 0.7991 (p90) REVERT: l 17 GLU cc_start: 0.7848 (mp0) cc_final: 0.7504 (mp0) REVERT: l 90 THR cc_start: 0.8642 (m) cc_final: 0.8286 (p) REVERT: l 94 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7557 (tt) REVERT: l 99 PHE cc_start: 0.7239 (m-80) cc_final: 0.6579 (m-80) outliers start: 60 outliers final: 42 residues processed: 313 average time/residue: 0.1100 time to fit residues: 50.0836 Evaluate side-chains 299 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 287 GLU Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain h residue 125 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 39 LEU Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 76 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 ASN b 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.108688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084233 restraints weight = 37150.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.087556 restraints weight = 20397.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.089750 restraints weight = 14642.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.091162 restraints weight = 11970.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.092007 restraints weight = 10526.641| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15642 Z= 0.141 Angle : 0.721 10.498 21390 Z= 0.341 Chirality : 0.043 0.265 2604 Planarity : 0.004 0.045 2514 Dihedral : 7.138 59.676 3903 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.44 % Allowed : 13.84 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.30 (0.21), residues: 1731 helix: 1.03 (0.29), residues: 375 sheet: 0.25 (0.25), residues: 420 loop : -0.92 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 422 TYR 0.021 0.001 TYR a 419 PHE 0.023 0.001 PHE J 87 TRP 0.056 0.002 TRP H 52 HIS 0.008 0.001 HIS c 305 Details of bonding type rmsd covalent geometry : bond 0.00308 (15516) covalent geometry : angle 0.66772 (21039) SS BOND : bond 0.00593 ( 27) SS BOND : angle 1.82045 ( 54) hydrogen bonds : bond 0.03635 ( 552) hydrogen bonds : angle 5.10656 ( 1566) link_ALPHA1-2 : bond 0.00017 ( 3) link_ALPHA1-2 : angle 2.06646 ( 9) link_ALPHA1-3 : bond 0.01659 ( 12) link_ALPHA1-3 : angle 3.28088 ( 36) link_ALPHA1-6 : bond 0.00971 ( 6) link_ALPHA1-6 : angle 1.53616 ( 18) link_BETA1-4 : bond 0.00805 ( 45) link_BETA1-4 : angle 2.46051 ( 135) link_NAG-ASN : bond 0.00327 ( 33) link_NAG-ASN : angle 1.68855 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7240 (pm20) cc_final: 0.6937 (mp0) REVERT: C 116 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8834 (mmmt) REVERT: C 156 ASP cc_start: 0.8031 (t70) cc_final: 0.7615 (t0) REVERT: C 161 LYS cc_start: 0.8707 (ttmt) cc_final: 0.8188 (tptt) REVERT: C 194 MET cc_start: 0.8939 (tpp) cc_final: 0.8336 (ttp) REVERT: C 214 MET cc_start: 0.7965 (ptp) cc_final: 0.7706 (ptp) REVERT: B 116 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8933 (mmmt) REVERT: B 151 GLU cc_start: 0.8185 (pm20) cc_final: 0.7953 (pm20) REVERT: B 161 LYS cc_start: 0.8530 (ttmt) cc_final: 0.7937 (tptt) REVERT: c 282 ARG cc_start: 0.8445 (tpt90) cc_final: 0.7969 (tpm170) REVERT: c 311 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7810 (t0) REVERT: c 419 TYR cc_start: 0.6945 (t80) cc_final: 0.6610 (t80) REVERT: c 420 MET cc_start: 0.7700 (mmt) cc_final: 0.6879 (tpt) REVERT: A 116 LYS cc_start: 0.9136 (mmtm) cc_final: 0.8899 (mmmt) REVERT: A 151 GLU cc_start: 0.8267 (pm20) cc_final: 0.8041 (pm20) REVERT: A 161 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8459 (ttpp) REVERT: A 194 MET cc_start: 0.8723 (tpp) cc_final: 0.8062 (ttm) REVERT: b 282 ARG cc_start: 0.8269 (tpt90) cc_final: 0.7607 (tpm170) REVERT: b 303 GLU cc_start: 0.7210 (tp30) cc_final: 0.6794 (tp30) REVERT: b 326 LEU cc_start: 0.8346 (mp) cc_final: 0.7895 (tp) REVERT: b 332 MET cc_start: 0.7755 (tpp) cc_final: 0.7302 (tpp) REVERT: b 418 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8508 (mt-10) REVERT: a 282 ARG cc_start: 0.8412 (tpt90) cc_final: 0.7855 (tpm170) REVERT: a 284 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8095 (mtp) REVERT: a 303 GLU cc_start: 0.6751 (tp30) cc_final: 0.6422 (tp30) REVERT: a 311 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7906 (t0) REVERT: a 326 LEU cc_start: 0.8116 (mt) cc_final: 0.7713 (mp) REVERT: a 332 MET cc_start: 0.7895 (tpp) cc_final: 0.7254 (tpp) REVERT: a 348 GLN cc_start: 0.4974 (mt0) cc_final: 0.4181 (tt0) REVERT: a 410 MET cc_start: 0.8029 (mtp) cc_final: 0.7674 (ttm) REVERT: a 420 MET cc_start: 0.8106 (mmt) cc_final: 0.7603 (tpt) REVERT: H 43 ARG cc_start: 0.8613 (ttp-170) cc_final: 0.8346 (mtm110) REVERT: H 53 ILE cc_start: 0.8455 (mt) cc_final: 0.7988 (mt) REVERT: H 98 ASP cc_start: 0.7523 (m-30) cc_final: 0.7130 (m-30) REVERT: L 17 GLU cc_start: 0.7560 (mp0) cc_final: 0.7220 (mp0) REVERT: L 18 ARG cc_start: 0.8500 (ttm170) cc_final: 0.7637 (ttp80) REVERT: L 94 LEU cc_start: 0.7826 (tp) cc_final: 0.7195 (tt) REVERT: L 99 PHE cc_start: 0.7243 (m-80) cc_final: 0.6545 (m-80) REVERT: L 102 TYR cc_start: 0.8185 (m-80) cc_final: 0.7901 (m-80) REVERT: J 5 GLN cc_start: 0.7138 (tp40) cc_final: 0.6777 (tp-100) REVERT: J 30 PHE cc_start: 0.8121 (t80) cc_final: 0.7816 (t80) REVERT: J 43 ARG cc_start: 0.8422 (ttp-170) cc_final: 0.8121 (mtm110) REVERT: J 52 TRP cc_start: 0.8087 (t60) cc_final: 0.7343 (t60) REVERT: J 98 ASP cc_start: 0.7047 (m-30) cc_final: 0.6654 (m-30) REVERT: K 17 GLU cc_start: 0.8152 (mp0) cc_final: 0.7276 (mp0) REVERT: K 42 TYR cc_start: 0.8630 (m-80) cc_final: 0.7910 (m-80) REVERT: K 90 THR cc_start: 0.8759 (m) cc_final: 0.8526 (p) REVERT: K 94 LEU cc_start: 0.7736 (tp) cc_final: 0.7335 (tt) REVERT: K 99 PHE cc_start: 0.7632 (m-80) cc_final: 0.6966 (m-80) REVERT: h 43 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8144 (mtm110) REVERT: h 52 TRP cc_start: 0.8050 (t60) cc_final: 0.7655 (t60) REVERT: h 53 ILE cc_start: 0.8411 (mt) cc_final: 0.7836 (mt) REVERT: h 85 ASN cc_start: 0.7343 (p0) cc_final: 0.7122 (p0) REVERT: h 87 PHE cc_start: 0.8490 (p90) cc_final: 0.8099 (p90) REVERT: l 17 GLU cc_start: 0.7968 (mp0) cc_final: 0.7630 (mp0) REVERT: l 90 THR cc_start: 0.8715 (m) cc_final: 0.8398 (p) REVERT: l 99 PHE cc_start: 0.7287 (m-80) cc_final: 0.6691 (m-80) outliers start: 53 outliers final: 34 residues processed: 314 average time/residue: 0.1119 time to fit residues: 51.6243 Evaluate side-chains 288 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 210 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 39 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 72 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.107777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083427 restraints weight = 37037.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.086692 restraints weight = 20564.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.088816 restraints weight = 14850.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.090197 restraints weight = 12189.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.090978 restraints weight = 10743.369| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15642 Z= 0.158 Angle : 0.733 11.404 21390 Z= 0.346 Chirality : 0.043 0.257 2604 Planarity : 0.004 0.053 2514 Dihedral : 6.901 57.138 3903 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.38 % Allowed : 13.97 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.33 (0.21), residues: 1731 helix: 1.06 (0.29), residues: 375 sheet: 0.19 (0.25), residues: 426 loop : -0.95 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG l 67 TYR 0.019 0.001 TYR a 419 PHE 0.011 0.001 PHE H 87 TRP 0.035 0.001 TRP H 52 HIS 0.007 0.001 HIS c 305 Details of bonding type rmsd covalent geometry : bond 0.00353 (15516) covalent geometry : angle 0.68200 (21039) SS BOND : bond 0.00610 ( 27) SS BOND : angle 1.76951 ( 54) hydrogen bonds : bond 0.03752 ( 552) hydrogen bonds : angle 5.03748 ( 1566) link_ALPHA1-2 : bond 0.00064 ( 3) link_ALPHA1-2 : angle 2.04626 ( 9) link_ALPHA1-3 : bond 0.01586 ( 12) link_ALPHA1-3 : angle 3.29954 ( 36) link_ALPHA1-6 : bond 0.00992 ( 6) link_ALPHA1-6 : angle 1.55991 ( 18) link_BETA1-4 : bond 0.00770 ( 45) link_BETA1-4 : angle 2.42027 ( 135) link_NAG-ASN : bond 0.00264 ( 33) link_NAG-ASN : angle 1.65670 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 270 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7264 (pm20) cc_final: 0.6696 (mp0) REVERT: C 156 ASP cc_start: 0.8187 (t70) cc_final: 0.7219 (t0) REVERT: C 161 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8340 (ttpp) REVERT: C 194 MET cc_start: 0.8943 (tpp) cc_final: 0.8295 (ttp) REVERT: C 214 MET cc_start: 0.7946 (ptp) cc_final: 0.7712 (ptp) REVERT: B 116 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8924 (mmmt) REVERT: B 151 GLU cc_start: 0.8141 (pm20) cc_final: 0.7928 (pm20) REVERT: B 161 LYS cc_start: 0.8580 (ttmt) cc_final: 0.7990 (tptt) REVERT: c 282 ARG cc_start: 0.8476 (tpt90) cc_final: 0.8001 (tpm170) REVERT: c 284 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8061 (mtm) REVERT: c 311 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7942 (t0) REVERT: c 348 GLN cc_start: 0.4895 (mt0) cc_final: 0.4251 (tt0) REVERT: c 419 TYR cc_start: 0.6993 (t80) cc_final: 0.6171 (t80) REVERT: c 420 MET cc_start: 0.7694 (mmt) cc_final: 0.6868 (tpt) REVERT: A 116 LYS cc_start: 0.9132 (mmtm) cc_final: 0.8906 (mmmt) REVERT: A 161 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8439 (ttpp) REVERT: b 284 MET cc_start: 0.8279 (mtm) cc_final: 0.7639 (mtm) REVERT: b 303 GLU cc_start: 0.7270 (tp30) cc_final: 0.6971 (tp30) REVERT: b 326 LEU cc_start: 0.8452 (mp) cc_final: 0.8011 (tp) REVERT: b 332 MET cc_start: 0.7656 (tpp) cc_final: 0.7308 (tpp) REVERT: b 351 MET cc_start: 0.9062 (tpp) cc_final: 0.8743 (mmm) REVERT: a 282 ARG cc_start: 0.8443 (tpt90) cc_final: 0.8022 (tpt170) REVERT: a 284 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8073 (mtp) REVERT: a 303 GLU cc_start: 0.6882 (tp30) cc_final: 0.6353 (tp30) REVERT: a 311 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7826 (t70) REVERT: a 326 LEU cc_start: 0.8153 (mt) cc_final: 0.7754 (mp) REVERT: a 348 GLN cc_start: 0.4971 (mt0) cc_final: 0.3956 (tt0) REVERT: a 410 MET cc_start: 0.8031 (mtp) cc_final: 0.7602 (ttm) REVERT: a 420 MET cc_start: 0.8198 (mmt) cc_final: 0.7628 (tpt) REVERT: H 5 GLN cc_start: 0.7315 (tp40) cc_final: 0.6877 (tp-100) REVERT: H 6 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6523 (mm-30) REVERT: H 19 LEU cc_start: 0.7939 (tt) cc_final: 0.7651 (tt) REVERT: H 43 ARG cc_start: 0.8608 (ttp-170) cc_final: 0.8313 (mtm110) REVERT: H 53 ILE cc_start: 0.8508 (mt) cc_final: 0.8045 (mt) REVERT: H 98 ASP cc_start: 0.7479 (m-30) cc_final: 0.7057 (m-30) REVERT: L 17 GLU cc_start: 0.7570 (mp0) cc_final: 0.7224 (mp0) REVERT: L 18 ARG cc_start: 0.8547 (ttm170) cc_final: 0.7569 (ttp80) REVERT: L 94 LEU cc_start: 0.7791 (tp) cc_final: 0.7178 (tt) REVERT: L 99 PHE cc_start: 0.7320 (m-80) cc_final: 0.6615 (m-80) REVERT: L 127 LYS cc_start: 0.7541 (pttt) cc_final: 0.7268 (ptpt) REVERT: J 5 GLN cc_start: 0.7140 (tp40) cc_final: 0.6780 (tp-100) REVERT: J 30 PHE cc_start: 0.8324 (t80) cc_final: 0.8059 (t80) REVERT: J 43 ARG cc_start: 0.8446 (ttp-170) cc_final: 0.8130 (mtm110) REVERT: J 52 TRP cc_start: 0.8018 (t60) cc_final: 0.7700 (t60) REVERT: J 98 ASP cc_start: 0.7167 (m-30) cc_final: 0.6779 (m-30) REVERT: K 17 GLU cc_start: 0.8178 (mp0) cc_final: 0.7301 (mp0) REVERT: K 42 TYR cc_start: 0.8640 (m-80) cc_final: 0.7942 (m-80) REVERT: K 90 THR cc_start: 0.8799 (m) cc_final: 0.8565 (p) REVERT: K 94 LEU cc_start: 0.7731 (tp) cc_final: 0.7312 (tt) REVERT: K 99 PHE cc_start: 0.7680 (m-80) cc_final: 0.7048 (m-80) REVERT: h 5 GLN cc_start: 0.7086 (tp40) cc_final: 0.6609 (tp-100) REVERT: h 43 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8191 (mtm110) REVERT: h 52 TRP cc_start: 0.8057 (t60) cc_final: 0.7607 (t60) REVERT: h 53 ILE cc_start: 0.8468 (mt) cc_final: 0.7870 (mt) REVERT: h 85 ASN cc_start: 0.7250 (p0) cc_final: 0.6989 (p0) REVERT: h 87 PHE cc_start: 0.8499 (p90) cc_final: 0.8053 (p90) REVERT: l 17 GLU cc_start: 0.7949 (mp0) cc_final: 0.7574 (mp0) REVERT: l 90 THR cc_start: 0.8750 (m) cc_final: 0.8431 (p) REVERT: l 99 PHE cc_start: 0.7353 (m-80) cc_final: 0.6860 (m-80) outliers start: 52 outliers final: 33 residues processed: 300 average time/residue: 0.1124 time to fit residues: 49.2649 Evaluate side-chains 292 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 210 TRP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 39 LEU Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.107879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083589 restraints weight = 37530.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086878 restraints weight = 20571.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.089023 restraints weight = 14737.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090402 restraints weight = 12050.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.091226 restraints weight = 10607.649| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15642 Z= 0.147 Angle : 0.723 11.477 21390 Z= 0.340 Chirality : 0.043 0.253 2604 Planarity : 0.004 0.050 2514 Dihedral : 6.563 44.557 3903 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.12 % Allowed : 14.29 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.28 (0.21), residues: 1731 helix: 1.12 (0.29), residues: 375 sheet: 0.22 (0.25), residues: 426 loop : -0.93 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG l 67 TYR 0.037 0.001 TYR b 419 PHE 0.012 0.001 PHE H 87 TRP 0.037 0.001 TRP H 52 HIS 0.007 0.001 HIS c 305 Details of bonding type rmsd covalent geometry : bond 0.00325 (15516) covalent geometry : angle 0.67499 (21039) SS BOND : bond 0.00636 ( 27) SS BOND : angle 1.62374 ( 54) hydrogen bonds : bond 0.03605 ( 552) hydrogen bonds : angle 4.98241 ( 1566) link_ALPHA1-2 : bond 0.00039 ( 3) link_ALPHA1-2 : angle 2.08767 ( 9) link_ALPHA1-3 : bond 0.01532 ( 12) link_ALPHA1-3 : angle 3.28486 ( 36) link_ALPHA1-6 : bond 0.01060 ( 6) link_ALPHA1-6 : angle 1.53538 ( 18) link_BETA1-4 : bond 0.00766 ( 45) link_BETA1-4 : angle 2.33069 ( 135) link_NAG-ASN : bond 0.00257 ( 33) link_NAG-ASN : angle 1.56679 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 271 time to evaluate : 0.540 Fit side-chains REVERT: C 156 ASP cc_start: 0.8079 (t70) cc_final: 0.7304 (t0) REVERT: C 161 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8370 (ttpp) REVERT: C 194 MET cc_start: 0.8940 (tpp) cc_final: 0.8338 (ttp) REVERT: B 116 LYS cc_start: 0.9151 (mmtm) cc_final: 0.8924 (mmmt) REVERT: B 161 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8216 (ttpp) REVERT: c 282 ARG cc_start: 0.8531 (tpt90) cc_final: 0.8008 (tpm170) REVERT: c 311 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7887 (t0) REVERT: c 348 GLN cc_start: 0.4865 (mt0) cc_final: 0.4264 (tt0) REVERT: c 419 TYR cc_start: 0.7046 (t80) cc_final: 0.6559 (t80) REVERT: c 420 MET cc_start: 0.7507 (mmt) cc_final: 0.6702 (tpt) REVERT: A 82 MET cc_start: 0.8980 (pmm) cc_final: 0.8388 (pmm) REVERT: A 116 LYS cc_start: 0.9111 (mmtm) cc_final: 0.8896 (mmmt) REVERT: A 151 GLU cc_start: 0.7991 (pm20) cc_final: 0.7758 (pt0) REVERT: A 161 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8468 (ttpp) REVERT: A 194 MET cc_start: 0.8636 (tpp) cc_final: 0.8099 (ttm) REVERT: b 282 ARG cc_start: 0.8386 (tpt90) cc_final: 0.7881 (tpm170) REVERT: b 284 MET cc_start: 0.8295 (mtm) cc_final: 0.7698 (mtm) REVERT: b 303 GLU cc_start: 0.7363 (tp30) cc_final: 0.7101 (tp30) REVERT: b 311 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7637 (t70) REVERT: b 326 LEU cc_start: 0.8448 (mp) cc_final: 0.8024 (tp) REVERT: b 351 MET cc_start: 0.9125 (tpp) cc_final: 0.8849 (mmm) REVERT: a 282 ARG cc_start: 0.8462 (tpt90) cc_final: 0.8056 (tpt170) REVERT: a 284 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8208 (mtp) REVERT: a 303 GLU cc_start: 0.6803 (tp30) cc_final: 0.6270 (tp30) REVERT: a 311 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7815 (t0) REVERT: a 326 LEU cc_start: 0.8192 (mt) cc_final: 0.7896 (mp) REVERT: a 332 MET cc_start: 0.7797 (tpp) cc_final: 0.7174 (tpp) REVERT: a 348 GLN cc_start: 0.4992 (mt0) cc_final: 0.4032 (tt0) REVERT: a 410 MET cc_start: 0.8054 (mtp) cc_final: 0.7582 (ttm) REVERT: a 420 MET cc_start: 0.8190 (mmt) cc_final: 0.7769 (tpt) REVERT: a 423 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: H 5 GLN cc_start: 0.7471 (tp40) cc_final: 0.7031 (tp-100) REVERT: H 19 LEU cc_start: 0.7884 (tt) cc_final: 0.7636 (tt) REVERT: H 21 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6759 (mm) REVERT: H 43 ARG cc_start: 0.8585 (ttp-170) cc_final: 0.8334 (mtm110) REVERT: H 53 ILE cc_start: 0.8477 (mt) cc_final: 0.8037 (mt) REVERT: H 98 ASP cc_start: 0.7494 (m-30) cc_final: 0.7071 (m-30) REVERT: L 17 GLU cc_start: 0.7600 (mp0) cc_final: 0.7260 (mp0) REVERT: L 18 ARG cc_start: 0.8550 (ttm170) cc_final: 0.7608 (ttp80) REVERT: L 94 LEU cc_start: 0.7799 (tp) cc_final: 0.7224 (tt) REVERT: L 99 PHE cc_start: 0.7399 (m-80) cc_final: 0.6769 (m-80) REVERT: L 127 LYS cc_start: 0.7576 (pttt) cc_final: 0.7320 (ptpt) REVERT: J 5 GLN cc_start: 0.7086 (tp40) cc_final: 0.6751 (tp-100) REVERT: J 30 PHE cc_start: 0.8364 (t80) cc_final: 0.8123 (t80) REVERT: J 43 ARG cc_start: 0.8495 (ttp-170) cc_final: 0.8142 (mtm110) REVERT: J 52 TRP cc_start: 0.8119 (t60) cc_final: 0.7667 (t60) REVERT: J 98 ASP cc_start: 0.7245 (m-30) cc_final: 0.6864 (m-30) REVERT: K 17 GLU cc_start: 0.8320 (mp0) cc_final: 0.7436 (mp0) REVERT: K 42 TYR cc_start: 0.8612 (m-80) cc_final: 0.7941 (m-80) REVERT: K 90 THR cc_start: 0.8857 (m) cc_final: 0.8623 (p) REVERT: K 94 LEU cc_start: 0.7594 (tp) cc_final: 0.7187 (tt) REVERT: K 99 PHE cc_start: 0.7537 (m-80) cc_final: 0.6958 (m-80) REVERT: h 5 GLN cc_start: 0.7101 (tp40) cc_final: 0.6624 (tp-100) REVERT: h 43 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8228 (mtm110) REVERT: h 53 ILE cc_start: 0.8497 (mt) cc_final: 0.7997 (mt) REVERT: h 87 PHE cc_start: 0.8490 (p90) cc_final: 0.8126 (p90) REVERT: h 118 TRP cc_start: 0.8554 (m100) cc_final: 0.8343 (m100) REVERT: l 17 GLU cc_start: 0.7987 (mp0) cc_final: 0.7603 (mp0) REVERT: l 90 THR cc_start: 0.8769 (m) cc_final: 0.8480 (p) REVERT: l 99 PHE cc_start: 0.7295 (m-80) cc_final: 0.6780 (m-80) REVERT: l 125 GLU cc_start: 0.5017 (tt0) cc_final: 0.4766 (tt0) outliers start: 48 outliers final: 28 residues processed: 294 average time/residue: 0.1142 time to fit residues: 48.7914 Evaluate side-chains 282 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 419 TYR Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain a residue 423 GLN Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.0030 chunk 117 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 423 GLN L 44 HIS K 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.104372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081236 restraints weight = 37184.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084667 restraints weight = 19171.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086948 restraints weight = 13083.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088456 restraints weight = 10320.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089437 restraints weight = 8841.995| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15642 Z= 0.145 Angle : 0.728 9.923 21390 Z= 0.342 Chirality : 0.043 0.249 2604 Planarity : 0.004 0.053 2514 Dihedral : 6.356 36.284 3903 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.34 % Allowed : 15.72 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.30 (0.21), residues: 1731 helix: 1.13 (0.29), residues: 375 sheet: 0.23 (0.25), residues: 423 loop : -0.96 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 67 TYR 0.034 0.001 TYR a 419 PHE 0.012 0.001 PHE H 87 TRP 0.028 0.001 TRP H 52 HIS 0.009 0.001 HIS L 44 Details of bonding type rmsd covalent geometry : bond 0.00323 (15516) covalent geometry : angle 0.68229 (21039) SS BOND : bond 0.00606 ( 27) SS BOND : angle 1.62677 ( 54) hydrogen bonds : bond 0.03584 ( 552) hydrogen bonds : angle 4.99063 ( 1566) link_ALPHA1-2 : bond 0.00081 ( 3) link_ALPHA1-2 : angle 2.07910 ( 9) link_ALPHA1-3 : bond 0.01494 ( 12) link_ALPHA1-3 : angle 3.23100 ( 36) link_ALPHA1-6 : bond 0.01156 ( 6) link_ALPHA1-6 : angle 1.55583 ( 18) link_BETA1-4 : bond 0.00749 ( 45) link_BETA1-4 : angle 2.28689 ( 135) link_NAG-ASN : bond 0.00222 ( 33) link_NAG-ASN : angle 1.56487 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7326 (mp0) cc_final: 0.6981 (mp0) REVERT: C 156 ASP cc_start: 0.8151 (t70) cc_final: 0.7327 (t0) REVERT: C 161 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8342 (ttpp) REVERT: C 194 MET cc_start: 0.8958 (tpp) cc_final: 0.8383 (ttp) REVERT: B 116 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8873 (mmmt) REVERT: B 161 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8218 (ttpp) REVERT: c 282 ARG cc_start: 0.8540 (tpt90) cc_final: 0.7986 (tpm170) REVERT: c 311 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7951 (t0) REVERT: c 348 GLN cc_start: 0.4773 (mt0) cc_final: 0.4206 (tt0) REVERT: c 419 TYR cc_start: 0.7400 (t80) cc_final: 0.6461 (t80) REVERT: c 420 MET cc_start: 0.7554 (mmt) cc_final: 0.6603 (tpt) REVERT: A 116 LYS cc_start: 0.9123 (mmtm) cc_final: 0.8921 (mmmt) REVERT: A 194 MET cc_start: 0.8697 (tpp) cc_final: 0.8105 (ttm) REVERT: b 282 ARG cc_start: 0.8326 (tpt90) cc_final: 0.7761 (tpm170) REVERT: b 284 MET cc_start: 0.8241 (mtm) cc_final: 0.7628 (mtm) REVERT: b 303 GLU cc_start: 0.7407 (tp30) cc_final: 0.7132 (tp30) REVERT: b 332 MET cc_start: 0.7666 (tpp) cc_final: 0.7183 (tpp) REVERT: b 351 MET cc_start: 0.9084 (tpp) cc_final: 0.8793 (mmm) REVERT: a 282 ARG cc_start: 0.8469 (tpt90) cc_final: 0.8046 (tpt170) REVERT: a 284 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8188 (mtp) REVERT: a 303 GLU cc_start: 0.6899 (tp30) cc_final: 0.6382 (tp30) REVERT: a 311 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7832 (t0) REVERT: a 326 LEU cc_start: 0.8252 (mt) cc_final: 0.7935 (mp) REVERT: a 332 MET cc_start: 0.7714 (tpp) cc_final: 0.7000 (tpp) REVERT: a 348 GLN cc_start: 0.4883 (mt0) cc_final: 0.3939 (tt0) REVERT: a 410 MET cc_start: 0.8019 (mtp) cc_final: 0.7550 (ttm) REVERT: a 420 MET cc_start: 0.8320 (mmt) cc_final: 0.7751 (tpt) REVERT: H 5 GLN cc_start: 0.7486 (tp40) cc_final: 0.6933 (tp-100) REVERT: H 19 LEU cc_start: 0.7890 (tt) cc_final: 0.7615 (tt) REVERT: H 21 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6712 (mm) REVERT: H 43 ARG cc_start: 0.8436 (ttp-170) cc_final: 0.8118 (mtm110) REVERT: H 53 ILE cc_start: 0.8405 (mt) cc_final: 0.7942 (mt) REVERT: H 90 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8307 (mtpp) REVERT: H 98 ASP cc_start: 0.7496 (m-30) cc_final: 0.7094 (m-30) REVERT: L 17 GLU cc_start: 0.7692 (mp0) cc_final: 0.7321 (mp0) REVERT: L 18 ARG cc_start: 0.8529 (ttm170) cc_final: 0.7584 (ttp80) REVERT: L 94 LEU cc_start: 0.7785 (tp) cc_final: 0.7182 (tt) REVERT: L 99 PHE cc_start: 0.7574 (m-80) cc_final: 0.6750 (m-80) REVERT: L 127 LYS cc_start: 0.7562 (pttt) cc_final: 0.7307 (ptpt) REVERT: J 5 GLN cc_start: 0.7070 (tp40) cc_final: 0.6748 (tp-100) REVERT: J 30 PHE cc_start: 0.8330 (t80) cc_final: 0.8058 (t80) REVERT: J 43 ARG cc_start: 0.8097 (ttp-170) cc_final: 0.7649 (mtm110) REVERT: J 52 TRP cc_start: 0.7881 (t60) cc_final: 0.7373 (t60) REVERT: J 98 ASP cc_start: 0.7243 (m-30) cc_final: 0.6797 (m-30) REVERT: K 17 GLU cc_start: 0.8295 (mp0) cc_final: 0.7430 (mp0) REVERT: K 42 TYR cc_start: 0.8463 (m-80) cc_final: 0.7889 (m-80) REVERT: K 90 THR cc_start: 0.8810 (m) cc_final: 0.8534 (p) REVERT: K 94 LEU cc_start: 0.7555 (tp) cc_final: 0.7121 (tt) REVERT: K 99 PHE cc_start: 0.7484 (m-80) cc_final: 0.6887 (m-80) REVERT: h 5 GLN cc_start: 0.7146 (tp40) cc_final: 0.6690 (tp-100) REVERT: h 43 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8147 (mtm110) REVERT: h 52 TRP cc_start: 0.7959 (t60) cc_final: 0.7567 (t60) REVERT: h 53 ILE cc_start: 0.8419 (mt) cc_final: 0.7865 (mt) REVERT: h 85 ASN cc_start: 0.7754 (p0) cc_final: 0.7139 (p0) REVERT: h 87 PHE cc_start: 0.8495 (p90) cc_final: 0.8087 (p90) REVERT: l 17 GLU cc_start: 0.8011 (mp0) cc_final: 0.7629 (mp0) REVERT: l 90 THR cc_start: 0.8804 (m) cc_final: 0.8447 (p) REVERT: l 99 PHE cc_start: 0.7269 (m-80) cc_final: 0.6729 (m-80) outliers start: 36 outliers final: 26 residues processed: 286 average time/residue: 0.1086 time to fit residues: 45.4305 Evaluate side-chains 279 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 160 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** c 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 423 GLN ** b 305 HIS ** 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 = 0.3609 r_free = 0.3609 target = 0.101341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.078308 restraints weight = 38396.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081575 restraints weight = 19833.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083751 restraints weight = 13661.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.085170 restraints weight = 10872.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.086021 restraints weight = 9384.945| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 15642 Z= 0.233 Angle : 0.815 9.605 21390 Z= 0.383 Chirality : 0.045 0.241 2604 Planarity : 0.005 0.067 2514 Dihedral : 6.681 36.676 3903 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 2.53 % Allowed : 16.37 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.49 (0.21), residues: 1731 helix: 0.98 (0.28), residues: 375 sheet: 0.14 (0.26), residues: 423 loop : -1.11 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG a 422 TYR 0.038 0.002 TYR a 419 PHE 0.027 0.002 PHE J 87 TRP 0.034 0.002 TRP H 52 HIS 0.005 0.001 HIS L 44 Details of bonding type rmsd covalent geometry : bond 0.00540 (15516) covalent geometry : angle 0.76846 (21039) SS BOND : bond 0.00770 ( 27) SS BOND : angle 1.83874 ( 54) hydrogen bonds : bond 0.04109 ( 552) hydrogen bonds : angle 5.16735 ( 1566) link_ALPHA1-2 : bond 0.00212 ( 3) link_ALPHA1-2 : angle 2.08809 ( 9) link_ALPHA1-3 : bond 0.01531 ( 12) link_ALPHA1-3 : angle 3.42137 ( 36) link_ALPHA1-6 : bond 0.01022 ( 6) link_ALPHA1-6 : angle 1.67009 ( 18) link_BETA1-4 : bond 0.00717 ( 45) link_BETA1-4 : angle 2.38222 ( 135) link_NAG-ASN : bond 0.00321 ( 33) link_NAG-ASN : angle 1.80842 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 GLU cc_start: 0.7468 (mp0) cc_final: 0.7172 (mp0) REVERT: C 156 ASP cc_start: 0.8322 (t70) cc_final: 0.7486 (t0) REVERT: C 161 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8440 (ttpp) REVERT: C 194 MET cc_start: 0.9017 (tpp) cc_final: 0.8305 (ttp) REVERT: B 116 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8938 (mmmt) REVERT: B 161 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8341 (ttpp) REVERT: B 251 ASP cc_start: 0.7493 (m-30) cc_final: 0.7197 (m-30) REVERT: c 282 ARG cc_start: 0.8624 (tpt90) cc_final: 0.8052 (tpm170) REVERT: c 311 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8104 (t0) REVERT: c 348 GLN cc_start: 0.4924 (mt0) cc_final: 0.4047 (tt0) REVERT: c 419 TYR cc_start: 0.6739 (t80) cc_final: 0.6376 (t80) REVERT: c 420 MET cc_start: 0.7540 (mmt) cc_final: 0.6667 (tpt) REVERT: A 116 LYS cc_start: 0.9183 (mmtm) cc_final: 0.8966 (mmmt) REVERT: A 151 GLU cc_start: 0.8286 (pm20) cc_final: 0.8052 (pt0) REVERT: A 161 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8439 (ttpp) REVERT: b 284 MET cc_start: 0.8346 (mtm) cc_final: 0.7652 (mtm) REVERT: b 311 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7669 (t70) REVERT: b 332 MET cc_start: 0.7887 (tpp) cc_final: 0.7359 (tpp) REVERT: b 351 MET cc_start: 0.9106 (tpp) cc_final: 0.8743 (mmm) REVERT: a 284 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8070 (mtp) REVERT: a 303 GLU cc_start: 0.7182 (tp30) cc_final: 0.6721 (tp30) REVERT: a 311 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7867 (t0) REVERT: a 332 MET cc_start: 0.7747 (tpp) cc_final: 0.6931 (tpp) REVERT: a 348 GLN cc_start: 0.4801 (mt0) cc_final: 0.4192 (tt0) REVERT: a 410 MET cc_start: 0.7922 (mtp) cc_final: 0.7477 (ttm) REVERT: a 420 MET cc_start: 0.8350 (mmt) cc_final: 0.7776 (tpt) REVERT: H 43 ARG cc_start: 0.8484 (ttp-170) cc_final: 0.8140 (mtm110) REVERT: H 53 ILE cc_start: 0.8349 (mt) cc_final: 0.7891 (mt) REVERT: H 95 THR cc_start: 0.8210 (t) cc_final: 0.7920 (p) REVERT: H 98 ASP cc_start: 0.7616 (m-30) cc_final: 0.7172 (m-30) REVERT: L 17 GLU cc_start: 0.7503 (mp0) cc_final: 0.7170 (mp0) REVERT: L 18 ARG cc_start: 0.8466 (ttm170) cc_final: 0.7447 (ttp80) REVERT: L 94 LEU cc_start: 0.7709 (tp) cc_final: 0.7023 (tt) REVERT: L 99 PHE cc_start: 0.7489 (m-80) cc_final: 0.6688 (m-80) REVERT: J 43 ARG cc_start: 0.8256 (ttp-170) cc_final: 0.7949 (mtm110) REVERT: J 52 TRP cc_start: 0.7949 (t60) cc_final: 0.7504 (t60) REVERT: J 98 ASP cc_start: 0.7332 (m-30) cc_final: 0.6951 (m-30) REVERT: J 117 VAL cc_start: 0.8652 (t) cc_final: 0.8387 (p) REVERT: K 17 GLU cc_start: 0.8244 (mp0) cc_final: 0.7699 (mp0) REVERT: K 42 TYR cc_start: 0.8698 (m-80) cc_final: 0.8027 (m-80) REVERT: K 90 THR cc_start: 0.8917 (m) cc_final: 0.8627 (p) REVERT: K 94 LEU cc_start: 0.7669 (tp) cc_final: 0.7249 (tt) REVERT: K 99 PHE cc_start: 0.7619 (m-80) cc_final: 0.6950 (m-80) REVERT: h 5 GLN cc_start: 0.7137 (tp40) cc_final: 0.6648 (tp-100) REVERT: h 43 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7930 (ttp80) REVERT: h 52 TRP cc_start: 0.7946 (t60) cc_final: 0.7526 (t60) REVERT: h 85 ASN cc_start: 0.7998 (p0) cc_final: 0.7475 (p0) REVERT: h 87 PHE cc_start: 0.8525 (p90) cc_final: 0.8036 (p90) REVERT: l 17 GLU cc_start: 0.8048 (mp0) cc_final: 0.7673 (mp0) REVERT: l 90 THR cc_start: 0.8747 (m) cc_final: 0.8280 (p) REVERT: l 99 PHE cc_start: 0.7431 (m-80) cc_final: 0.6853 (m-80) outliers start: 39 outliers final: 30 residues processed: 264 average time/residue: 0.1311 time to fit residues: 50.3218 Evaluate side-chains 273 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 TRP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain b residue 292 CYS Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain a residue 284 MET Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain h residue 21 LEU Chi-restraints excluded: chain h residue 104 CYS Chi-restraints excluded: chain h residue 125 THR Chi-restraints excluded: chain l residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 50 optimal weight: 0.0570 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.100743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.077576 restraints weight = 37570.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080866 restraints weight = 19444.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083047 restraints weight = 13359.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084475 restraints weight = 10619.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085336 restraints weight = 9161.745| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15642 Z= 0.200 Angle : 0.779 9.389 21390 Z= 0.366 Chirality : 0.044 0.252 2604 Planarity : 0.004 0.060 2514 Dihedral : 6.637 37.708 3903 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 2.53 % Allowed : 16.70 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.55 (0.21), residues: 1731 helix: 1.01 (0.28), residues: 375 sheet: 0.07 (0.26), residues: 423 loop : -1.16 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 67 TYR 0.038 0.002 TYR a 419 PHE 0.027 0.002 PHE l 76 TRP 0.033 0.002 TRP H 52 HIS 0.006 0.001 HIS c 305 Details of bonding type rmsd covalent geometry : bond 0.00457 (15516) covalent geometry : angle 0.73203 (21039) SS BOND : bond 0.00723 ( 27) SS BOND : angle 1.73091 ( 54) hydrogen bonds : bond 0.03896 ( 552) hydrogen bonds : angle 5.17302 ( 1566) link_ALPHA1-2 : bond 0.00188 ( 3) link_ALPHA1-2 : angle 2.17560 ( 9) link_ALPHA1-3 : bond 0.01553 ( 12) link_ALPHA1-3 : angle 3.38752 ( 36) link_ALPHA1-6 : bond 0.01042 ( 6) link_ALPHA1-6 : angle 1.67503 ( 18) link_BETA1-4 : bond 0.00731 ( 45) link_BETA1-4 : angle 2.31283 ( 135) link_NAG-ASN : bond 0.00249 ( 33) link_NAG-ASN : angle 1.75516 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2286.71 seconds wall clock time: 40 minutes 39.71 seconds (2439.71 seconds total)