Starting phenix.real_space_refine on Mon Jul 28 06:46:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejg_28181/07_2025/8ejg_28181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejg_28181/07_2025/8ejg_28181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejg_28181/07_2025/8ejg_28181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejg_28181/07_2025/8ejg_28181.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejg_28181/07_2025/8ejg_28181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejg_28181/07_2025/8ejg_28181.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 6174 2.51 5 N 1530 2.21 5 O 2172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9966 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "a" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "b" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "c" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "D" 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 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: "H" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 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: "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: "L" 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: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 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: "Q" 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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 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: 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: "Z" 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: "d" 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 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: "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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.08, per 1000 atoms: 0.71 Number of scatterers: 9966 At special positions: 0 Unit cell: (101.2, 102.35, 104.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2172 8.00 N 1530 7.00 C 6174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.04 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.16 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS a 359 " distance=2.02 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.03 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.01 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.04 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.16 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS b 359 " distance=2.02 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.04 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.16 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 211 " distance=2.04 Simple disulfide: pdb=" SG CYS C 206 " - pdb=" SG CYS c 359 " distance=2.02 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.03 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " distance=2.01 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.03 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.01 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 K 4 " - " MAN K 5 " " MAN d 4 " - " MAN d 5 " " MAN f 4 " - " MAN f 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA K 3 " - " MAN K 4 " " MAN K 6 " - " MAN K 7 " " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA K 3 " - " MAN K 6 " " BMA M 3 " - " MAN M 5 " " BMA T 3 " - " MAN T 5 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 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 " - " BGC G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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 P 1 " - " NAG P 2 " " NAG P 2 " - " BGC P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BGC W 3 " " 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 Z 2 " - " BMA Z 3 " " 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 f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " NAG-ASN " NAG D 1 " - " ASN A 78 " " NAG E 1 " - " ASN A 88 " " NAG F 1 " - " ASN A 98 " " NAG G 1 " - " ASN A 108 " " NAG H 1 " - " ASN A 118 " " NAG I 1 " - " ASN A 166 " " NAG J 1 " - " ASN A 223 " " NAG K 1 " - " ASN a 364 " " NAG L 1 " - " ASN a 372 " " NAG M 1 " - " ASN B 78 " " NAG N 1 " - " ASN B 88 " " NAG O 1 " - " ASN B 98 " " NAG P 1 " - " ASN B 108 " " NAG Q 1 " - " ASN B 118 " " NAG R 1 " - " ASN B 166 " " NAG S 1 " - " ASN B 223 " " NAG T 1 " - " ASN C 78 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 98 " " NAG W 1 " - " ASN C 108 " " NAG X 1 " - " ASN C 118 " " NAG Y 1 " - " ASN C 166 " " NAG Z 1 " - " ASN C 223 " " NAG a 501 " - " ASN a 389 " " NAG a 502 " - " ASN a 394 " " NAG b 501 " - " ASN b 389 " " NAG b 502 " - " ASN b 394 " " NAG c 501 " - " ASN c 389 " " NAG c 502 " - " ASN c 394 " " NAG d 1 " - " ASN b 364 " " NAG e 1 " - " ASN b 372 " " NAG f 1 " - " ASN c 364 " " NAG g 1 " - " ASN c 372 " Time building additional restraints: 4.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 41.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.680A pdb=" N THR A 76 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'a' and resid 263 through 269 Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 299 through 302 Processing helix chain 'a' and resid 306 through 324 Processing helix chain 'a' and resid 335 through 340 Processing helix chain 'a' and resid 341 through 343 No H-bonds generated for 'chain 'a' and resid 341 through 343' Processing helix chain 'a' and resid 345 through 358 removed outlier: 3.649A pdb=" N ILE a 349 " --> pdb=" O ASN a 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 421 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.682A pdb=" N THR B 76 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 129 through 142 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 237 through 245 Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.681A pdb=" N THR C 76 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 129 through 142 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 237 through 245 Processing helix chain 'b' and resid 263 through 269 Processing helix chain 'b' and resid 293 through 298 Processing helix chain 'b' and resid 299 through 302 Processing helix chain 'b' and resid 306 through 324 Processing helix chain 'b' and resid 335 through 340 Processing helix chain 'b' and resid 341 through 343 No H-bonds generated for 'chain 'b' and resid 341 through 343' Processing helix chain 'b' and resid 345 through 358 removed outlier: 3.648A pdb=" N ILE b 349 " --> pdb=" O ASN b 345 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 421 Processing helix chain 'c' and resid 263 through 269 Processing helix chain 'c' and resid 293 through 298 Processing helix chain 'c' and resid 299 through 302 Processing helix chain 'c' and resid 306 through 324 Processing helix chain 'c' and resid 335 through 340 Processing helix chain 'c' and resid 341 through 343 No H-bonds generated for 'chain 'c' and resid 341 through 343' Processing helix chain 'c' and resid 345 through 358 removed outlier: 3.648A pdb=" N ILE c 349 " --> pdb=" O ASN c 345 " (cutoff:3.500A) Processing helix chain 'c' and resid 398 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR A 86 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG A 234 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 387 through 388 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR B 86 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ARG B 234 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR C 86 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG C 234 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 387 through 388 Processing sheet with id=AA9, first strand: chain 'c' and resid 387 through 388 378 hydrogen bonds defined for protein. 990 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: 2.80 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2577 1.33 - 1.47: 3187 1.47 - 1.60: 4251 1.60 - 1.74: 11 1.74 - 1.88: 132 Bond restraints: 10158 Sorted by residual: bond pdb=" NE1 TRP c 385 " pdb=" CE2 TRP c 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.15e+01 bond pdb=" NE1 TRP a 385 " pdb=" CE2 TRP a 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.15e+01 bond pdb=" NE1 TRP b 385 " pdb=" CE2 TRP b 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.13e+01 bond pdb=" CB LEU A 59 " pdb=" CG LEU A 59 " ideal model delta sigma weight residual 1.530 1.668 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" CB LEU C 59 " pdb=" CG LEU C 59 " ideal model delta sigma weight residual 1.530 1.668 -0.138 2.00e-02 2.50e+03 4.75e+01 ... (remaining 10153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.42: 13719 7.42 - 14.84: 30 14.84 - 22.26: 3 22.26 - 29.67: 0 29.67 - 37.09: 3 Bond angle restraints: 13755 Sorted by residual: angle pdb=" C2 NAG b 502 " pdb=" N2 NAG b 502 " pdb=" C7 NAG b 502 " ideal model delta sigma weight residual 124.56 161.65 -37.09 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C2 NAG c 502 " pdb=" N2 NAG c 502 " pdb=" C7 NAG c 502 " ideal model delta sigma weight residual 124.56 161.59 -37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" C2 NAG a 502 " pdb=" N2 NAG a 502 " pdb=" C7 NAG a 502 " ideal model delta sigma weight residual 124.56 161.59 -37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" CA PHE a 398 " pdb=" CB PHE a 398 " pdb=" CG PHE a 398 " ideal model delta sigma weight residual 113.80 122.30 -8.50 1.00e+00 1.00e+00 7.23e+01 angle pdb=" CA PHE b 398 " pdb=" CB PHE b 398 " pdb=" CG PHE b 398 " ideal model delta sigma weight residual 113.80 122.30 -8.50 1.00e+00 1.00e+00 7.22e+01 ... (remaining 13750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 6813 21.44 - 42.88: 264 42.88 - 64.33: 79 64.33 - 85.77: 134 85.77 - 107.21: 84 Dihedral angle restraints: 7374 sinusoidal: 4200 harmonic: 3174 Sorted by residual: dihedral pdb=" C PHE a 398 " pdb=" N PHE a 398 " pdb=" CA PHE a 398 " pdb=" CB PHE a 398 " ideal model delta harmonic sigma weight residual -122.60 -111.92 -10.68 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C PHE b 398 " pdb=" N PHE b 398 " pdb=" CA PHE b 398 " pdb=" CB PHE b 398 " ideal model delta harmonic sigma weight residual -122.60 -111.94 -10.66 0 2.50e+00 1.60e-01 1.82e+01 dihedral pdb=" C PHE c 398 " pdb=" N PHE c 398 " pdb=" CA PHE c 398 " pdb=" CB PHE c 398 " ideal model delta harmonic sigma weight residual -122.60 -111.95 -10.65 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 7371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1047 0.108 - 0.216: 410 0.216 - 0.325: 211 0.325 - 0.433: 100 0.433 - 0.541: 44 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.61e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.59e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 ... (remaining 1809 not shown) Planarity restraints: 1629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 98 " -0.038 2.00e-02 2.50e+03 4.19e-02 2.19e+01 pdb=" CG ASN C 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN C 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 98 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " -0.038 2.00e-02 2.50e+03 4.19e-02 2.19e+01 pdb=" CG ASN A 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 98 " -0.038 2.00e-02 2.50e+03 4.18e-02 2.18e+01 pdb=" CG ASN B 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 98 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.050 2.00e-02 2.50e+03 ... (remaining 1626 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 303 2.66 - 3.22: 9737 3.22 - 3.78: 15061 3.78 - 4.34: 21516 4.34 - 4.90: 33333 Nonbonded interactions: 79950 Sorted by model distance: nonbonded pdb=" NH1 ARG a 378 " pdb=" O THR a 379 " model vdw 2.106 3.120 nonbonded pdb=" NH1 ARG b 378 " pdb=" O THR b 379 " model vdw 2.107 3.120 nonbonded pdb=" NH1 ARG c 378 " pdb=" O THR c 379 " model vdw 2.109 3.120 nonbonded pdb=" N HIS c 397 " pdb=" O HIS c 397 " model vdw 2.286 2.496 nonbonded pdb=" N HIS a 397 " pdb=" O HIS a 397 " model vdw 2.286 2.496 ... (remaining 79945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'T' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) } ncs_group { reference = chain 'F' selection = chain 'O' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'd' selection = chain 'f' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.630 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.026 0.138 10281 Z= 1.388 Angle : 2.059 37.092 14103 Z= 1.161 Chirality : 0.172 0.541 1812 Planarity : 0.009 0.051 1596 Dihedral : 20.946 107.210 5271 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.24), residues: 1071 helix: -1.09 (0.22), residues: 423 sheet: 1.26 (0.50), residues: 102 loop : -0.71 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.007 TRP A 226 HIS 0.008 0.002 HIS B 91 PHE 0.024 0.006 PHE b 261 TYR 0.055 0.008 TYR A 240 ARG 0.008 0.001 ARG A 95 Details of bonding type rmsd link_NAG-ASN : bond 0.07530 ( 33) link_NAG-ASN : angle 2.60422 ( 99) link_ALPHA1-6 : bond 0.05259 ( 6) link_ALPHA1-6 : angle 3.46290 ( 18) link_BETA1-4 : bond 0.07505 ( 51) link_BETA1-4 : angle 6.04600 ( 153) link_ALPHA1-2 : bond 0.07660 ( 3) link_ALPHA1-2 : angle 4.26510 ( 9) link_ALPHA1-3 : bond 0.07983 ( 9) link_ALPHA1-3 : angle 4.50889 ( 27) hydrogen bonds : bond 0.16477 ( 378) hydrogen bonds : angle 7.06040 ( 990) SS BOND : bond 0.04909 ( 21) SS BOND : angle 3.77771 ( 42) covalent geometry : bond 0.02537 (10158) covalent geometry : angle 1.94434 (13755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 305 ASP cc_start: 0.6570 (p0) cc_final: 0.6359 (p0) REVERT: a 330 GLN cc_start: 0.7109 (mp10) cc_final: 0.6559 (pp30) REVERT: b 305 ASP cc_start: 0.6440 (p0) cc_final: 0.6091 (p0) REVERT: c 305 ASP cc_start: 0.6753 (p0) cc_final: 0.6429 (p0) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2951 time to fit residues: 124.8475 Evaluate side-chains 180 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 222 GLN a 304 HIS ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 341 ASN B 91 HIS C 91 HIS b 304 HIS b 404 GLN c 304 HIS ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 347 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.090106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.064270 restraints weight = 27763.607| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 4.38 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10281 Z= 0.237 Angle : 1.133 19.164 14103 Z= 0.503 Chirality : 0.056 0.419 1812 Planarity : 0.005 0.036 1596 Dihedral : 17.886 86.745 3228 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.16 % Favored : 93.65 % Rotamer: Outliers : 2.38 % Allowed : 12.01 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1071 helix: -0.29 (0.25), residues: 426 sheet: 1.90 (0.51), residues: 114 loop : -1.09 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 263 HIS 0.007 0.002 HIS B 140 PHE 0.021 0.002 PHE c 261 TYR 0.018 0.002 TYR c 277 ARG 0.005 0.001 ARG c 378 Details of bonding type rmsd link_NAG-ASN : bond 0.00783 ( 33) link_NAG-ASN : angle 2.75400 ( 99) link_ALPHA1-6 : bond 0.00638 ( 6) link_ALPHA1-6 : angle 1.55881 ( 18) link_BETA1-4 : bond 0.02064 ( 51) link_BETA1-4 : angle 5.12594 ( 153) link_ALPHA1-2 : bond 0.00459 ( 3) link_ALPHA1-2 : angle 1.84150 ( 9) link_ALPHA1-3 : bond 0.01627 ( 9) link_ALPHA1-3 : angle 1.23436 ( 27) hydrogen bonds : bond 0.05782 ( 378) hydrogen bonds : angle 5.24702 ( 990) SS BOND : bond 0.00412 ( 21) SS BOND : angle 1.53036 ( 42) covalent geometry : bond 0.00478 (10158) covalent geometry : angle 0.97612 (13755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8216 (tp30) cc_final: 0.7712 (mm-30) REVERT: A 152 MET cc_start: 0.8129 (ttt) cc_final: 0.7889 (ttt) REVERT: a 323 GLN cc_start: 0.8580 (tt0) cc_final: 0.8369 (tm-30) REVERT: a 330 GLN cc_start: 0.7666 (mp10) cc_final: 0.7417 (pp30) REVERT: a 347 GLN cc_start: 0.7391 (tt0) cc_final: 0.7182 (mt0) REVERT: B 74 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8486 (mmt) REVERT: B 94 ILE cc_start: 0.9057 (mt) cc_final: 0.8836 (tt) REVERT: C 94 ILE cc_start: 0.9071 (mt) cc_final: 0.8817 (tt) REVERT: C 99 GLU cc_start: 0.8402 (tp30) cc_final: 0.8124 (mm-30) REVERT: C 193 MET cc_start: 0.8811 (mmm) cc_final: 0.8531 (tpp) REVERT: b 326 LYS cc_start: 0.8022 (tppt) cc_final: 0.7773 (tppt) REVERT: b 330 GLN cc_start: 0.8548 (mp-120) cc_final: 0.8290 (mp10) REVERT: b 341 ASN cc_start: 0.9180 (m-40) cc_final: 0.8755 (m-40) REVERT: b 404 GLN cc_start: 0.8635 (tp40) cc_final: 0.8344 (tp-100) REVERT: c 305 ASP cc_start: 0.7576 (p0) cc_final: 0.7280 (p0) REVERT: c 378 ARG cc_start: 0.7947 (ttm-80) cc_final: 0.7538 (ttm-80) REVERT: c 401 ASP cc_start: 0.8922 (m-30) cc_final: 0.8712 (m-30) REVERT: c 407 ASP cc_start: 0.8629 (m-30) cc_final: 0.8206 (m-30) outliers start: 23 outliers final: 11 residues processed: 232 average time/residue: 0.2363 time to fit residues: 74.7511 Evaluate side-chains 189 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 341 ASN Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 288 GLU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 375 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 30.0000 chunk 80 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 96 optimal weight: 0.0770 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 422 GLN c 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.090333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.064756 restraints weight = 28549.965| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.31 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10281 Z= 0.197 Angle : 1.027 18.449 14103 Z= 0.443 Chirality : 0.053 0.402 1812 Planarity : 0.004 0.053 1596 Dihedral : 14.418 76.038 3228 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.38 % Favored : 92.34 % Rotamer: Outliers : 2.80 % Allowed : 13.98 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1071 helix: 0.02 (0.25), residues: 414 sheet: 2.35 (0.52), residues: 96 loop : -1.47 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 263 HIS 0.008 0.001 HIS A 178 PHE 0.017 0.002 PHE b 398 TYR 0.013 0.001 TYR A 149 ARG 0.011 0.001 ARG b 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 33) link_NAG-ASN : angle 2.80096 ( 99) link_ALPHA1-6 : bond 0.00865 ( 6) link_ALPHA1-6 : angle 1.57322 ( 18) link_BETA1-4 : bond 0.01827 ( 51) link_BETA1-4 : angle 4.74749 ( 153) link_ALPHA1-2 : bond 0.00247 ( 3) link_ALPHA1-2 : angle 1.73749 ( 9) link_ALPHA1-3 : bond 0.01480 ( 9) link_ALPHA1-3 : angle 1.27985 ( 27) hydrogen bonds : bond 0.04647 ( 378) hydrogen bonds : angle 5.14895 ( 990) SS BOND : bond 0.00500 ( 21) SS BOND : angle 1.69285 ( 42) covalent geometry : bond 0.00398 (10158) covalent geometry : angle 0.87058 (13755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 1.135 Fit side-chains REVERT: A 99 GLU cc_start: 0.8231 (tp30) cc_final: 0.7723 (mm-30) REVERT: A 155 ASP cc_start: 0.8440 (p0) cc_final: 0.7988 (p0) REVERT: A 169 HIS cc_start: 0.6874 (t70) cc_final: 0.6449 (t-90) REVERT: A 188 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8490 (mm-40) REVERT: a 347 GLN cc_start: 0.7302 (tt0) cc_final: 0.7022 (mt0) REVERT: a 400 ASP cc_start: 0.8330 (p0) cc_final: 0.7867 (p0) REVERT: B 79 MET cc_start: 0.8540 (mmm) cc_final: 0.8139 (mmm) REVERT: B 99 GLU cc_start: 0.8388 (tp30) cc_final: 0.8078 (mm-30) REVERT: C 94 ILE cc_start: 0.8968 (mt) cc_final: 0.8691 (tt) REVERT: C 99 GLU cc_start: 0.8481 (tp30) cc_final: 0.8193 (mm-30) REVERT: C 193 MET cc_start: 0.8770 (mmm) cc_final: 0.8368 (tpp) REVERT: C 213 MET cc_start: 0.8035 (mmt) cc_final: 0.7737 (mmp) REVERT: C 227 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7807 (mm-30) REVERT: C 246 GLN cc_start: 0.7902 (pp30) cc_final: 0.7126 (pp30) REVERT: b 326 LYS cc_start: 0.8067 (tppt) cc_final: 0.7854 (tppt) REVERT: b 341 ASN cc_start: 0.9236 (m-40) cc_final: 0.8864 (m-40) REVERT: b 404 GLN cc_start: 0.8857 (tp40) cc_final: 0.8392 (tp-100) REVERT: c 305 ASP cc_start: 0.7545 (p0) cc_final: 0.7238 (p0) REVERT: c 326 LYS cc_start: 0.8404 (tppt) cc_final: 0.8122 (tppt) REVERT: c 330 GLN cc_start: 0.8729 (mp10) cc_final: 0.8465 (mp10) REVERT: c 331 MET cc_start: 0.6685 (mmp) cc_final: 0.6355 (mmp) REVERT: c 378 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7793 (ttm-80) REVERT: c 400 ASP cc_start: 0.8701 (p0) cc_final: 0.8306 (p0) outliers start: 27 outliers final: 15 residues processed: 220 average time/residue: 0.2407 time to fit residues: 72.7971 Evaluate side-chains 192 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 288 GLU Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 53 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 61 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 422 GLN B 140 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.090583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.064787 restraints weight = 28411.654| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 4.31 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10281 Z= 0.170 Angle : 0.967 18.354 14103 Z= 0.415 Chirality : 0.051 0.400 1812 Planarity : 0.004 0.042 1596 Dihedral : 11.851 67.445 3228 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.47 % Favored : 92.25 % Rotamer: Outliers : 2.38 % Allowed : 14.60 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1071 helix: 0.16 (0.26), residues: 414 sheet: 2.31 (0.54), residues: 96 loop : -1.51 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 263 HIS 0.005 0.001 HIS B 92 PHE 0.017 0.002 PHE b 398 TYR 0.010 0.001 TYR C 65 ARG 0.006 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 33) link_NAG-ASN : angle 2.52198 ( 99) link_ALPHA1-6 : bond 0.01047 ( 6) link_ALPHA1-6 : angle 1.60709 ( 18) link_BETA1-4 : bond 0.01780 ( 51) link_BETA1-4 : angle 4.53422 ( 153) link_ALPHA1-2 : bond 0.00195 ( 3) link_ALPHA1-2 : angle 1.71891 ( 9) link_ALPHA1-3 : bond 0.01469 ( 9) link_ALPHA1-3 : angle 1.31710 ( 27) hydrogen bonds : bond 0.04079 ( 378) hydrogen bonds : angle 4.97714 ( 990) SS BOND : bond 0.00429 ( 21) SS BOND : angle 1.41950 ( 42) covalent geometry : bond 0.00322 (10158) covalent geometry : angle 0.81776 (13755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8213 (tp30) cc_final: 0.7711 (mm-30) REVERT: A 188 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8480 (mm-40) REVERT: a 323 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7933 (tm-30) REVERT: a 326 LYS cc_start: 0.8237 (tppt) cc_final: 0.7974 (tptp) REVERT: a 400 ASP cc_start: 0.8207 (p0) cc_final: 0.7611 (p0) REVERT: a 418 TYR cc_start: 0.5490 (t80) cc_final: 0.5118 (t80) REVERT: B 74 MET cc_start: 0.8835 (mmt) cc_final: 0.8609 (mmt) REVERT: B 79 MET cc_start: 0.8485 (mmm) cc_final: 0.8067 (mmm) REVERT: B 99 GLU cc_start: 0.8436 (tp30) cc_final: 0.8140 (mm-30) REVERT: B 124 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8585 (mtmm) REVERT: B 227 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7678 (mm-30) REVERT: B 249 ARG cc_start: 0.7110 (ttm-80) cc_final: 0.6504 (mtm-85) REVERT: C 79 MET cc_start: 0.8766 (mtp) cc_final: 0.8508 (mmt) REVERT: C 94 ILE cc_start: 0.8971 (mt) cc_final: 0.8672 (tt) REVERT: C 99 GLU cc_start: 0.8492 (tp30) cc_final: 0.8232 (mm-30) REVERT: C 156 PHE cc_start: 0.9228 (m-80) cc_final: 0.8935 (m-80) REVERT: C 191 MET cc_start: 0.8711 (mmm) cc_final: 0.8003 (tpt) REVERT: C 193 MET cc_start: 0.8809 (mmm) cc_final: 0.8412 (tpp) REVERT: C 213 MET cc_start: 0.7867 (mmt) cc_final: 0.7588 (mmp) REVERT: C 227 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7940 (mm-30) REVERT: C 246 GLN cc_start: 0.7916 (pp30) cc_final: 0.7590 (pp30) REVERT: b 341 ASN cc_start: 0.9233 (m-40) cc_final: 0.8804 (m-40) REVERT: b 404 GLN cc_start: 0.8873 (tp40) cc_final: 0.8436 (tp-100) REVERT: c 305 ASP cc_start: 0.7328 (p0) cc_final: 0.7074 (p0) REVERT: c 330 GLN cc_start: 0.8692 (mp10) cc_final: 0.8474 (mp10) REVERT: c 331 MET cc_start: 0.6820 (mmp) cc_final: 0.6521 (mmp) REVERT: c 338 LYS cc_start: 0.9120 (mtmm) cc_final: 0.8871 (mptt) REVERT: c 400 ASP cc_start: 0.8700 (p0) cc_final: 0.8247 (p0) outliers start: 23 outliers final: 13 residues processed: 213 average time/residue: 0.2455 time to fit residues: 71.3860 Evaluate side-chains 188 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 288 GLU Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 344 ILE Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 81 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** a 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.087989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.062054 restraints weight = 28710.299| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 4.32 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10281 Z= 0.261 Angle : 0.979 18.342 14103 Z= 0.426 Chirality : 0.053 0.379 1812 Planarity : 0.004 0.041 1596 Dihedral : 10.893 63.991 3228 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.78 % Favored : 90.94 % Rotamer: Outliers : 2.80 % Allowed : 15.22 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1071 helix: 0.23 (0.26), residues: 408 sheet: 1.99 (0.53), residues: 96 loop : -1.61 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 263 HIS 0.005 0.001 HIS A 123 PHE 0.018 0.002 PHE b 398 TYR 0.012 0.002 TYR B 65 ARG 0.009 0.001 ARG C 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 33) link_NAG-ASN : angle 2.60504 ( 99) link_ALPHA1-6 : bond 0.01027 ( 6) link_ALPHA1-6 : angle 1.80914 ( 18) link_BETA1-4 : bond 0.01752 ( 51) link_BETA1-4 : angle 4.52034 ( 153) link_ALPHA1-2 : bond 0.00164 ( 3) link_ALPHA1-2 : angle 1.76373 ( 9) link_ALPHA1-3 : bond 0.01378 ( 9) link_ALPHA1-3 : angle 1.51142 ( 27) hydrogen bonds : bond 0.04241 ( 378) hydrogen bonds : angle 4.86022 ( 990) SS BOND : bond 0.00601 ( 21) SS BOND : angle 1.39068 ( 42) covalent geometry : bond 0.00549 (10158) covalent geometry : angle 0.83110 (13755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8321 (tp30) cc_final: 0.7818 (mm-30) REVERT: A 188 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8448 (mm-40) REVERT: a 323 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7986 (tm-30) REVERT: a 326 LYS cc_start: 0.8240 (tppt) cc_final: 0.7975 (tptp) REVERT: a 346 ASP cc_start: 0.9092 (p0) cc_final: 0.8782 (p0) REVERT: a 400 ASP cc_start: 0.8440 (p0) cc_final: 0.8129 (p0) REVERT: a 418 TYR cc_start: 0.5378 (t80) cc_final: 0.5116 (t80) REVERT: B 74 MET cc_start: 0.8999 (mmt) cc_final: 0.8732 (mmt) REVERT: B 99 GLU cc_start: 0.8527 (tp30) cc_final: 0.8206 (mm-30) REVERT: B 124 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8611 (mtmm) REVERT: B 227 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7722 (mm-30) REVERT: C 79 MET cc_start: 0.8824 (mtp) cc_final: 0.8488 (mmt) REVERT: C 94 ILE cc_start: 0.9082 (mt) cc_final: 0.8773 (tt) REVERT: C 99 GLU cc_start: 0.8461 (tp30) cc_final: 0.8173 (mm-30) REVERT: C 156 PHE cc_start: 0.9257 (m-80) cc_final: 0.9010 (m-80) REVERT: C 193 MET cc_start: 0.8889 (mmm) cc_final: 0.8616 (tpp) REVERT: C 227 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7894 (mm-30) REVERT: C 246 GLN cc_start: 0.7910 (pp30) cc_final: 0.7480 (pp30) REVERT: b 326 LYS cc_start: 0.8017 (tppt) cc_final: 0.7805 (tppt) REVERT: b 341 ASN cc_start: 0.9278 (m-40) cc_final: 0.8889 (m-40) REVERT: b 404 GLN cc_start: 0.8957 (tp40) cc_final: 0.8461 (tp-100) REVERT: c 331 MET cc_start: 0.6963 (mmt) cc_final: 0.6757 (mmp) REVERT: c 338 LYS cc_start: 0.9204 (mtmm) cc_final: 0.8863 (mptt) REVERT: c 400 ASP cc_start: 0.8794 (p0) cc_final: 0.8490 (p0) outliers start: 27 outliers final: 20 residues processed: 205 average time/residue: 0.2419 time to fit residues: 67.3883 Evaluate side-chains 191 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN a 330 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.088964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.063299 restraints weight = 28341.727| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 4.31 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10281 Z= 0.164 Angle : 0.922 18.032 14103 Z= 0.402 Chirality : 0.050 0.371 1812 Planarity : 0.004 0.043 1596 Dihedral : 9.968 58.476 3228 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.19 % Favored : 92.53 % Rotamer: Outliers : 2.59 % Allowed : 15.63 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.25), residues: 1071 helix: 0.23 (0.26), residues: 417 sheet: 1.84 (0.53), residues: 96 loop : -1.59 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 263 HIS 0.005 0.001 HIS A 169 PHE 0.017 0.001 PHE b 398 TYR 0.014 0.001 TYR B 65 ARG 0.008 0.001 ARG b 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 33) link_NAG-ASN : angle 2.46517 ( 99) link_ALPHA1-6 : bond 0.01203 ( 6) link_ALPHA1-6 : angle 1.72229 ( 18) link_BETA1-4 : bond 0.01718 ( 51) link_BETA1-4 : angle 4.29812 ( 153) link_ALPHA1-2 : bond 0.00094 ( 3) link_ALPHA1-2 : angle 1.82371 ( 9) link_ALPHA1-3 : bond 0.01479 ( 9) link_ALPHA1-3 : angle 1.49382 ( 27) hydrogen bonds : bond 0.03836 ( 378) hydrogen bonds : angle 4.67580 ( 990) SS BOND : bond 0.00433 ( 21) SS BOND : angle 1.25658 ( 42) covalent geometry : bond 0.00311 (10158) covalent geometry : angle 0.77857 (13755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8328 (tp30) cc_final: 0.7857 (mm-30) REVERT: A 188 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8386 (mm-40) REVERT: a 323 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8036 (tm-30) REVERT: a 346 ASP cc_start: 0.9101 (p0) cc_final: 0.8741 (p0) REVERT: a 400 ASP cc_start: 0.8512 (p0) cc_final: 0.8045 (p0) REVERT: a 418 TYR cc_start: 0.5336 (t80) cc_final: 0.4773 (t80) REVERT: B 99 GLU cc_start: 0.8508 (tp30) cc_final: 0.8140 (mm-30) REVERT: B 124 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8636 (mtmm) REVERT: B 188 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8565 (mm-40) REVERT: B 227 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7604 (mm-30) REVERT: C 79 MET cc_start: 0.8812 (mtp) cc_final: 0.8536 (mmm) REVERT: C 94 ILE cc_start: 0.8946 (mt) cc_final: 0.8672 (tt) REVERT: C 99 GLU cc_start: 0.8501 (tp30) cc_final: 0.8282 (mm-30) REVERT: C 142 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8592 (p) REVERT: C 156 PHE cc_start: 0.9259 (m-80) cc_final: 0.9015 (m-80) REVERT: C 193 MET cc_start: 0.8824 (mmm) cc_final: 0.8529 (tpp) REVERT: C 227 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7991 (mm-30) REVERT: C 246 GLN cc_start: 0.8002 (pp30) cc_final: 0.7688 (pp30) REVERT: b 326 LYS cc_start: 0.8063 (tppt) cc_final: 0.7776 (tppt) REVERT: b 341 ASN cc_start: 0.9261 (m-40) cc_final: 0.8919 (m-40) REVERT: b 404 GLN cc_start: 0.8915 (tp40) cc_final: 0.8437 (tp-100) REVERT: c 326 LYS cc_start: 0.8372 (tppt) cc_final: 0.8110 (tppt) REVERT: c 338 LYS cc_start: 0.9148 (mtmm) cc_final: 0.8744 (mptt) REVERT: c 400 ASP cc_start: 0.8848 (p0) cc_final: 0.8400 (p0) outliers start: 25 outliers final: 15 residues processed: 213 average time/residue: 0.2682 time to fit residues: 78.3736 Evaluate side-chains 193 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 330 GLN Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain c residue 344 ILE Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 96 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 246 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.087720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.061978 restraints weight = 28908.079| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.40 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10281 Z= 0.223 Angle : 0.949 17.954 14103 Z= 0.417 Chirality : 0.051 0.370 1812 Planarity : 0.004 0.041 1596 Dihedral : 9.616 57.429 3228 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.78 % Favored : 90.94 % Rotamer: Outliers : 2.90 % Allowed : 16.56 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.26), residues: 1071 helix: 0.31 (0.26), residues: 411 sheet: 1.16 (0.52), residues: 114 loop : -1.67 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 263 HIS 0.005 0.001 HIS A 123 PHE 0.016 0.002 PHE b 398 TYR 0.024 0.001 TYR B 65 ARG 0.010 0.001 ARG c 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 33) link_NAG-ASN : angle 2.41780 ( 99) link_ALPHA1-6 : bond 0.01160 ( 6) link_ALPHA1-6 : angle 1.88664 ( 18) link_BETA1-4 : bond 0.01679 ( 51) link_BETA1-4 : angle 4.28647 ( 153) link_ALPHA1-2 : bond 0.00046 ( 3) link_ALPHA1-2 : angle 1.79783 ( 9) link_ALPHA1-3 : bond 0.01339 ( 9) link_ALPHA1-3 : angle 1.63158 ( 27) hydrogen bonds : bond 0.03981 ( 378) hydrogen bonds : angle 4.63850 ( 990) SS BOND : bond 0.00485 ( 21) SS BOND : angle 1.32424 ( 42) covalent geometry : bond 0.00466 (10158) covalent geometry : angle 0.81250 (13755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8372 (tp30) cc_final: 0.7906 (mm-30) REVERT: A 188 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8372 (mm-40) REVERT: A 246 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.7015 (pp30) REVERT: a 323 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8147 (tm-30) REVERT: a 346 ASP cc_start: 0.9119 (p0) cc_final: 0.8777 (p0) REVERT: a 400 ASP cc_start: 0.8475 (p0) cc_final: 0.7960 (p0) REVERT: B 74 MET cc_start: 0.8979 (mmt) cc_final: 0.8633 (mmm) REVERT: B 99 GLU cc_start: 0.8537 (tp30) cc_final: 0.8158 (mm-30) REVERT: B 124 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8639 (mtmm) REVERT: B 188 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8584 (mm-40) REVERT: B 227 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7674 (mm-30) REVERT: C 94 ILE cc_start: 0.8998 (mt) cc_final: 0.8681 (tt) REVERT: C 99 GLU cc_start: 0.8460 (tp30) cc_final: 0.8029 (mm-30) REVERT: C 142 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8654 (p) REVERT: C 156 PHE cc_start: 0.9230 (m-80) cc_final: 0.9014 (m-80) REVERT: C 193 MET cc_start: 0.8864 (mmm) cc_final: 0.8500 (tpp) REVERT: C 227 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8085 (mm-30) REVERT: b 341 ASN cc_start: 0.9125 (m-40) cc_final: 0.8779 (m-40) REVERT: b 404 GLN cc_start: 0.8959 (tp40) cc_final: 0.8468 (tp-100) REVERT: c 326 LYS cc_start: 0.8218 (tppt) cc_final: 0.7726 (tppt) REVERT: c 338 LYS cc_start: 0.9205 (mtmm) cc_final: 0.8780 (mptt) REVERT: c 400 ASP cc_start: 0.8905 (p0) cc_final: 0.8387 (p0) outliers start: 28 outliers final: 23 residues processed: 201 average time/residue: 0.2406 time to fit residues: 65.9020 Evaluate side-chains 197 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain b residue 420 ASP Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 332 SER Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS c 330 GLN ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.087947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.062117 restraints weight = 28959.528| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.38 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10281 Z= 0.196 Angle : 0.947 17.944 14103 Z= 0.419 Chirality : 0.051 0.366 1812 Planarity : 0.004 0.042 1596 Dihedral : 9.346 55.375 3228 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.94 % Favored : 91.78 % Rotamer: Outliers : 2.90 % Allowed : 16.56 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1071 helix: 0.29 (0.26), residues: 417 sheet: 1.28 (0.53), residues: 96 loop : -1.64 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 263 HIS 0.004 0.001 HIS A 123 PHE 0.016 0.002 PHE b 398 TYR 0.023 0.001 TYR B 65 ARG 0.008 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 33) link_NAG-ASN : angle 2.59182 ( 99) link_ALPHA1-6 : bond 0.01214 ( 6) link_ALPHA1-6 : angle 1.86091 ( 18) link_BETA1-4 : bond 0.01670 ( 51) link_BETA1-4 : angle 4.20970 ( 153) link_ALPHA1-2 : bond 0.00050 ( 3) link_ALPHA1-2 : angle 1.85622 ( 9) link_ALPHA1-3 : bond 0.01388 ( 9) link_ALPHA1-3 : angle 1.63645 ( 27) hydrogen bonds : bond 0.03919 ( 378) hydrogen bonds : angle 4.55492 ( 990) SS BOND : bond 0.00502 ( 21) SS BOND : angle 1.20776 ( 42) covalent geometry : bond 0.00402 (10158) covalent geometry : angle 0.81145 (13755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.883 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8380 (tp30) cc_final: 0.7908 (mm-30) REVERT: A 188 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8378 (mm-40) REVERT: A 249 ARG cc_start: 0.6643 (mtt90) cc_final: 0.6224 (mpt90) REVERT: a 323 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8204 (tm-30) REVERT: a 346 ASP cc_start: 0.9128 (p0) cc_final: 0.8783 (p0) REVERT: a 400 ASP cc_start: 0.8472 (p0) cc_final: 0.7968 (p0) REVERT: B 99 GLU cc_start: 0.8546 (tp30) cc_final: 0.8169 (mm-30) REVERT: B 188 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8572 (mm-40) REVERT: B 227 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7654 (mm-30) REVERT: C 94 ILE cc_start: 0.8963 (mt) cc_final: 0.8659 (tt) REVERT: C 99 GLU cc_start: 0.8455 (tp30) cc_final: 0.8040 (mm-30) REVERT: C 142 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8639 (p) REVERT: C 150 GLU cc_start: 0.8704 (pm20) cc_final: 0.8080 (tm-30) REVERT: C 227 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8030 (mm-30) REVERT: b 341 ASN cc_start: 0.9124 (m-40) cc_final: 0.8808 (m-40) REVERT: b 404 GLN cc_start: 0.8967 (tp40) cc_final: 0.8528 (tp-100) REVERT: c 326 LYS cc_start: 0.8374 (tppt) cc_final: 0.8086 (tppt) REVERT: c 330 GLN cc_start: 0.8832 (mm110) cc_final: 0.8559 (mm110) REVERT: c 338 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8749 (mptt) REVERT: c 400 ASP cc_start: 0.8913 (p0) cc_final: 0.8394 (p0) outliers start: 28 outliers final: 20 residues processed: 200 average time/residue: 0.2421 time to fit residues: 65.9062 Evaluate side-chains 193 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 332 SER Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 344 ILE Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 0.0050 chunk 70 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 169 HIS ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.087979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.062219 restraints weight = 28784.681| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.36 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10281 Z= 0.197 Angle : 0.979 17.934 14103 Z= 0.439 Chirality : 0.051 0.363 1812 Planarity : 0.005 0.042 1596 Dihedral : 9.070 53.298 3228 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.22 % Favored : 91.50 % Rotamer: Outliers : 2.59 % Allowed : 17.91 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.26), residues: 1071 helix: 0.26 (0.26), residues: 417 sheet: 0.72 (0.52), residues: 114 loop : -1.60 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 209 HIS 0.005 0.001 HIS B 123 PHE 0.033 0.002 PHE C 116 TYR 0.020 0.001 TYR c 418 ARG 0.008 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 33) link_NAG-ASN : angle 2.55199 ( 99) link_ALPHA1-6 : bond 0.01242 ( 6) link_ALPHA1-6 : angle 1.86196 ( 18) link_BETA1-4 : bond 0.01658 ( 51) link_BETA1-4 : angle 4.14400 ( 153) link_ALPHA1-2 : bond 0.00059 ( 3) link_ALPHA1-2 : angle 1.87555 ( 9) link_ALPHA1-3 : bond 0.01392 ( 9) link_ALPHA1-3 : angle 1.67384 ( 27) hydrogen bonds : bond 0.03924 ( 378) hydrogen bonds : angle 4.66312 ( 990) SS BOND : bond 0.00649 ( 21) SS BOND : angle 2.15727 ( 42) covalent geometry : bond 0.00411 (10158) covalent geometry : angle 0.84723 (13755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8381 (tp30) cc_final: 0.7911 (mm-30) REVERT: A 188 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8355 (mm-40) REVERT: A 246 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6903 (pp30) REVERT: A 249 ARG cc_start: 0.6563 (mtt90) cc_final: 0.5999 (mtt90) REVERT: a 346 ASP cc_start: 0.9091 (p0) cc_final: 0.8762 (p0) REVERT: a 400 ASP cc_start: 0.8504 (p0) cc_final: 0.8126 (p0) REVERT: B 74 MET cc_start: 0.8908 (mmt) cc_final: 0.8609 (mmm) REVERT: B 99 GLU cc_start: 0.8570 (tp30) cc_final: 0.8182 (mm-30) REVERT: B 188 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8554 (mm-40) REVERT: B 227 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7639 (mm-30) REVERT: C 94 ILE cc_start: 0.9026 (mt) cc_final: 0.8715 (tt) REVERT: C 99 GLU cc_start: 0.8467 (tp30) cc_final: 0.8049 (mm-30) REVERT: C 150 GLU cc_start: 0.8666 (pm20) cc_final: 0.7991 (tm-30) REVERT: C 193 MET cc_start: 0.9032 (tpp) cc_final: 0.8673 (tpp) REVERT: C 227 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8033 (mm-30) REVERT: b 341 ASN cc_start: 0.9139 (m-40) cc_final: 0.8829 (m-40) REVERT: b 404 GLN cc_start: 0.8977 (tp40) cc_final: 0.8534 (tp-100) REVERT: c 338 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8742 (mptt) REVERT: c 400 ASP cc_start: 0.8907 (p0) cc_final: 0.8620 (p0) outliers start: 25 outliers final: 20 residues processed: 199 average time/residue: 0.2724 time to fit residues: 74.1953 Evaluate side-chains 190 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 332 SER Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 0.0010 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 HIS ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 373 HIS ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.088845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.063138 restraints weight = 28759.425| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.36 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 10281 Z= 0.176 Angle : 0.991 20.776 14103 Z= 0.442 Chirality : 0.050 0.365 1812 Planarity : 0.004 0.043 1596 Dihedral : 8.799 52.886 3228 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.94 % Favored : 91.78 % Rotamer: Outliers : 1.35 % Allowed : 19.57 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.26), residues: 1071 helix: 0.25 (0.25), residues: 417 sheet: 0.65 (0.53), residues: 114 loop : -1.58 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 263 HIS 0.004 0.001 HIS A 123 PHE 0.017 0.002 PHE b 398 TYR 0.017 0.001 TYR C 65 ARG 0.008 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 33) link_NAG-ASN : angle 2.43000 ( 99) link_ALPHA1-6 : bond 0.01310 ( 6) link_ALPHA1-6 : angle 1.76861 ( 18) link_BETA1-4 : bond 0.01669 ( 51) link_BETA1-4 : angle 4.07046 ( 153) link_ALPHA1-2 : bond 0.00026 ( 3) link_ALPHA1-2 : angle 1.91288 ( 9) link_ALPHA1-3 : bond 0.01459 ( 9) link_ALPHA1-3 : angle 1.64565 ( 27) hydrogen bonds : bond 0.03766 ( 378) hydrogen bonds : angle 4.70772 ( 990) SS BOND : bond 0.00508 ( 21) SS BOND : angle 2.96168 ( 42) covalent geometry : bond 0.00367 (10158) covalent geometry : angle 0.86098 (13755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8376 (tp30) cc_final: 0.7913 (mm-30) REVERT: A 188 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8371 (mm-40) REVERT: A 192 ARG cc_start: 0.8789 (mtp85) cc_final: 0.8474 (mtp85) REVERT: A 249 ARG cc_start: 0.6787 (mtt90) cc_final: 0.6399 (mpt90) REVERT: a 346 ASP cc_start: 0.9071 (p0) cc_final: 0.8724 (p0) REVERT: a 400 ASP cc_start: 0.8459 (p0) cc_final: 0.8110 (p0) REVERT: B 74 MET cc_start: 0.8848 (mmt) cc_final: 0.8538 (mmm) REVERT: B 99 GLU cc_start: 0.8507 (tp30) cc_final: 0.8139 (mm-30) REVERT: B 188 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8520 (mm-40) REVERT: B 227 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7645 (mm-30) REVERT: C 62 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8923 (mmmm) REVERT: C 94 ILE cc_start: 0.8893 (mt) cc_final: 0.8632 (tt) REVERT: C 99 GLU cc_start: 0.8496 (tp30) cc_final: 0.8142 (mm-30) REVERT: C 150 GLU cc_start: 0.8635 (pm20) cc_final: 0.7955 (tm-30) REVERT: C 193 MET cc_start: 0.9048 (tpp) cc_final: 0.8679 (tpp) REVERT: C 227 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8030 (mm-30) REVERT: b 341 ASN cc_start: 0.9132 (m-40) cc_final: 0.8836 (m-40) REVERT: c 338 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8716 (mptt) REVERT: c 400 ASP cc_start: 0.8856 (p0) cc_final: 0.8556 (p0) outliers start: 13 outliers final: 9 residues processed: 192 average time/residue: 0.2635 time to fit residues: 68.1670 Evaluate side-chains 189 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 344 ILE Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 103 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN a 373 HIS ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.087736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.062191 restraints weight = 28401.901| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.29 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 10281 Z= 0.208 Angle : 0.984 18.657 14103 Z= 0.438 Chirality : 0.051 0.363 1812 Planarity : 0.004 0.043 1596 Dihedral : 8.690 53.415 3228 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.40 % Favored : 91.22 % Rotamer: Outliers : 1.45 % Allowed : 19.05 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.26), residues: 1071 helix: 0.22 (0.26), residues: 417 sheet: 0.49 (0.52), residues: 114 loop : -1.58 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 263 HIS 0.005 0.001 HIS A 123 PHE 0.017 0.002 PHE b 398 TYR 0.016 0.001 TYR B 65 ARG 0.008 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 33) link_NAG-ASN : angle 2.43843 ( 99) link_ALPHA1-6 : bond 0.01262 ( 6) link_ALPHA1-6 : angle 1.83649 ( 18) link_BETA1-4 : bond 0.01656 ( 51) link_BETA1-4 : angle 4.06611 ( 153) link_ALPHA1-2 : bond 0.00074 ( 3) link_ALPHA1-2 : angle 1.89598 ( 9) link_ALPHA1-3 : bond 0.01337 ( 9) link_ALPHA1-3 : angle 1.71942 ( 27) hydrogen bonds : bond 0.03838 ( 378) hydrogen bonds : angle 4.67899 ( 990) SS BOND : bond 0.00635 ( 21) SS BOND : angle 2.55131 ( 42) covalent geometry : bond 0.00442 (10158) covalent geometry : angle 0.85609 (13755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4359.01 seconds wall clock time: 78 minutes 58.56 seconds (4738.56 seconds total)