Starting phenix.real_space_refine on Tue May 13 09:43:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejf_28180/05_2025/8ejf_28180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejf_28180/05_2025/8ejf_28180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejf_28180/05_2025/8ejf_28180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejf_28180/05_2025/8ejf_28180.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejf_28180/05_2025/8ejf_28180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejf_28180/05_2025/8ejf_28180.cif" } resolution = 3.72 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= 0.017 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 6081 2.51 5 N 1530 2.21 5 O 2100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9801 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1560 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "a" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1321 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain: "B" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1560 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "b" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1321 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain: "C" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1560 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "c" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1321 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 4, 'TRANS': 158} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" 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: "O" 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: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "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: 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: "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: 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: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 6.96, per 1000 atoms: 0.71 Number of scatterers: 9801 At special positions: 0 Unit cell: (94.05, 91.96, 107.635, 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 2100 8.00 N 1530 7.00 C 6081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=1.80 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.02 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=1.80 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.02 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=1.80 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.02 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.02 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 4 " " BMA T 3 " - " MAN T 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " " BMA O 3 " - " MAN O 5 " " BMA R 3 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA W 3 " - " MAN W 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 3 " " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG A 501 " - " ASN A 99 " " NAG B 501 " - " ASN B 99 " " NAG C 501 " - " ASN C 99 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 109 " " NAG G 1 " - " ASN A 119 " " NAG H 1 " - " ASN A 167 " " NAG I 1 " - " ASN A 224 " " NAG J 1 " - " ASN a 365 " " NAG K 1 " - " ASN a 373 " " NAG L 1 " - " ASN B 79 " " NAG M 1 " - " ASN B 89 " " NAG N 1 " - " ASN B 109 " " NAG O 1 " - " ASN B 119 " " NAG P 1 " - " ASN B 167 " " NAG Q 1 " - " ASN B 224 " " NAG R 1 " - " ASN b 365 " " NAG S 1 " - " ASN b 373 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 89 " " NAG V 1 " - " ASN C 109 " " NAG W 1 " - " ASN C 119 " " NAG X 1 " - " ASN C 167 " " NAG Y 1 " - " ASN C 224 " " NAG Z 1 " - " ASN c 365 " " NAG a 701 " - " ASN a 390 " " NAG a 702 " - " ASN a 395 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " " NAG d 1 " - " ASN c 373 " Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 958.4 milliseconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 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: 39 helices and 12 sheets defined 36.7% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.647A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.184A pdb=" N ILE A 201 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'a' and resid 295 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 327 Processing helix chain 'a' and resid 333 through 345 removed outlier: 3.611A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 Processing helix chain 'a' and resid 395 through 400 Processing helix chain 'a' and resid 400 through 417 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.647A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 4.183A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'b' and resid 295 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 327 Processing helix chain 'b' and resid 333 through 345 removed outlier: 3.611A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 Processing helix chain 'b' and resid 395 through 400 Processing helix chain 'b' and resid 400 through 417 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.647A pdb=" N GLY C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 4.184A pdb=" N ILE C 201 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'c' and resid 295 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 327 Processing helix chain 'c' and resid 333 through 345 removed outlier: 3.611A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 Processing helix chain 'c' and resid 395 through 400 Processing helix chain 'c' and resid 400 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.758A pdb=" N HIS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 154 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 277 through 280 Processing sheet with id=AA4, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.758A pdb=" N HIS B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 154 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 277 through 280 Processing sheet with id=AA8, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 84 through 89 removed outlier: 6.758A pdb=" N HIS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 154 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 277 through 280 Processing sheet with id=AB3, first strand: chain 'c' and resid 388 through 389 333 hydrogen bonds defined for protein. 891 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: 2.42 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1848 1.32 - 1.46: 3260 1.46 - 1.59: 4724 1.59 - 1.73: 32 1.73 - 1.87: 129 Bond restraints: 9993 Sorted by residual: bond pdb=" NE ARG b 422 " pdb=" CZ ARG b 422 " ideal model delta sigma weight residual 1.326 1.407 -0.081 1.10e-02 8.26e+03 5.41e+01 bond pdb=" NE ARG c 422 " pdb=" CZ ARG c 422 " ideal model delta sigma weight residual 1.326 1.407 -0.081 1.10e-02 8.26e+03 5.40e+01 bond pdb=" NE ARG a 422 " pdb=" CZ ARG a 422 " ideal model delta sigma weight residual 1.326 1.407 -0.081 1.10e-02 8.26e+03 5.39e+01 bond pdb=" CB PHE a 399 " pdb=" CG PHE a 399 " ideal model delta sigma weight residual 1.502 1.373 0.129 2.30e-02 1.89e+03 3.17e+01 bond pdb=" CB PHE c 399 " pdb=" CG PHE c 399 " ideal model delta sigma weight residual 1.502 1.373 0.129 2.30e-02 1.89e+03 3.16e+01 ... (remaining 9988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 11867 2.90 - 5.81: 1434 5.81 - 8.71: 208 8.71 - 11.61: 24 11.61 - 14.52: 3 Bond angle restraints: 13536 Sorted by residual: angle pdb=" N ILE b 345 " pdb=" CA ILE b 345 " pdb=" C ILE b 345 " ideal model delta sigma weight residual 112.29 123.82 -11.53 9.40e-01 1.13e+00 1.50e+02 angle pdb=" N ILE c 345 " pdb=" CA ILE c 345 " pdb=" C ILE c 345 " ideal model delta sigma weight residual 112.29 123.80 -11.51 9.40e-01 1.13e+00 1.50e+02 angle pdb=" N ILE a 345 " pdb=" CA ILE a 345 " pdb=" C ILE a 345 " ideal model delta sigma weight residual 112.29 123.80 -11.51 9.40e-01 1.13e+00 1.50e+02 angle pdb=" N SER A 171 " pdb=" CA SER A 171 " pdb=" C SER A 171 " ideal model delta sigma weight residual 114.31 99.79 14.52 1.29e+00 6.01e-01 1.27e+02 angle pdb=" N SER B 171 " pdb=" CA SER B 171 " pdb=" C SER B 171 " ideal model delta sigma weight residual 114.31 99.79 14.52 1.29e+00 6.01e-01 1.27e+02 ... (remaining 13531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 6735 21.24 - 42.49: 216 42.49 - 63.73: 42 63.73 - 84.97: 63 84.97 - 106.21: 66 Dihedral angle restraints: 7122 sinusoidal: 3951 harmonic: 3171 Sorted by residual: dihedral pdb=" CA CYS C 118 " pdb=" CB CYS C 118 " pdb=" SG CYS C 118 " pdb=" SG CYS C 155 " ideal model delta sinusoidal sigma weight residual 79.00 5.99 73.01 1 2.00e+01 2.50e-03 1.70e+01 dihedral pdb=" CA CYS A 118 " pdb=" CB CYS A 118 " pdb=" SG CYS A 118 " pdb=" SG CYS A 155 " ideal model delta sinusoidal sigma weight residual 79.00 6.01 72.99 1 2.00e+01 2.50e-03 1.70e+01 dihedral pdb=" CA CYS B 118 " pdb=" CB CYS B 118 " pdb=" SG CYS B 118 " pdb=" SG CYS B 155 " ideal model delta sinusoidal sigma weight residual 79.00 6.03 72.97 1 2.00e+01 2.50e-03 1.70e+01 ... (remaining 7119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 988 0.106 - 0.212: 421 0.212 - 0.318: 215 0.318 - 0.423: 106 0.423 - 0.529: 25 Chirality restraints: 1755 Sorted by residual: chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 2.62 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 MAN W 4 " pdb=" O3 BMA W 3 " pdb=" C2 MAN W 4 " pdb=" O5 MAN W 4 " both_signs ideal model delta sigma weight residual False 2.40 2.61 -0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 MAN O 4 " pdb=" O3 BMA O 3 " pdb=" C2 MAN O 4 " pdb=" O5 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.40 2.61 -0.21 2.00e-02 2.50e+03 1.13e+02 ... (remaining 1752 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN a 395 " -0.069 2.00e-02 2.50e+03 7.02e-02 6.17e+01 pdb=" CG ASN a 395 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN a 395 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN a 395 " 0.108 2.00e-02 2.50e+03 pdb=" C1 NAG a 702 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN b 395 " 0.068 2.00e-02 2.50e+03 7.02e-02 6.16e+01 pdb=" CG ASN b 395 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN b 395 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN b 395 " -0.108 2.00e-02 2.50e+03 pdb=" C1 NAG b 702 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN c 395 " -0.068 2.00e-02 2.50e+03 7.01e-02 6.14e+01 pdb=" CG ASN c 395 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN c 395 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN c 395 " 0.107 2.00e-02 2.50e+03 pdb=" C1 NAG c 702 " -0.085 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2691 2.82 - 3.34: 9986 3.34 - 3.86: 16323 3.86 - 4.38: 20471 4.38 - 4.90: 30916 Nonbonded interactions: 80387 Sorted by model distance: nonbonded pdb=" N SER B 171 " pdb=" N TYR B 172 " model vdw 2.299 2.560 nonbonded pdb=" N SER A 171 " pdb=" N TYR A 172 " model vdw 2.299 2.560 nonbonded pdb=" N SER C 171 " pdb=" N TYR C 172 " model vdw 2.300 2.560 nonbonded pdb=" N ASP b 347 " pdb=" OD1 ASP b 347 " model vdw 2.378 3.120 nonbonded pdb=" N ASP c 347 " pdb=" OD1 ASP c 347 " model vdw 2.379 3.120 ... (remaining 80382 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.310 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.226 10104 Z= 1.330 Angle : 2.097 15.649 13848 Z= 1.272 Chirality : 0.164 0.529 1755 Planarity : 0.011 0.049 1587 Dihedral : 17.178 106.214 5019 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -1.87 (0.23), residues: 1068 helix: -1.24 (0.24), residues: 384 sheet: -0.18 (0.57), residues: 87 loop : -1.38 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.008 TRP B 210 HIS 0.011 0.003 HIS B 93 PHE 0.018 0.006 PHE c 309 TYR 0.088 0.011 TYR C 166 ARG 0.007 0.001 ARG c 314 Details of bonding type rmsd link_NAG-ASN : bond 0.07677 ( 33) link_NAG-ASN : angle 3.91803 ( 99) link_ALPHA1-6 : bond 0.05090 ( 9) link_ALPHA1-6 : angle 2.42488 ( 27) link_BETA1-4 : bond 0.07316 ( 36) link_BETA1-4 : angle 5.29219 ( 108) link_ALPHA1-3 : bond 0.09424 ( 9) link_ALPHA1-3 : angle 7.21873 ( 27) hydrogen bonds : bond 0.17340 ( 333) hydrogen bonds : angle 7.75561 ( 891) link_BETA1-6 : bond 0.08822 ( 3) link_BETA1-6 : angle 7.74284 ( 9) SS BOND : bond 0.08596 ( 21) SS BOND : angle 3.06833 ( 42) covalent geometry : bond 0.02407 ( 9993) covalent geometry : angle 1.99469 (13536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 312 MET cc_start: 0.8327 (mmm) cc_final: 0.8093 (tpp) REVERT: b 359 MET cc_start: 0.8390 (mmm) cc_final: 0.8004 (mmm) REVERT: C 82 MET cc_start: 0.8895 (pmm) cc_final: 0.8468 (pmm) REVERT: c 359 MET cc_start: 0.8275 (mmm) cc_final: 0.7709 (tpp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3213 time to fit residues: 92.0115 Evaluate side-chains 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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: 5.9990 chunk 79 optimal weight: 0.0030 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 HIS a 406 GLN B 92 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 GLN C 92 HIS ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.055009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.043436 restraints weight = 54549.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.044854 restraints weight = 31132.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.045801 restraints weight = 22244.671| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 10104 Z= 0.244 Angle : 1.134 10.898 13848 Z= 0.542 Chirality : 0.051 0.302 1755 Planarity : 0.005 0.034 1587 Dihedral : 16.031 92.760 2988 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.58 % Favored : 89.33 % Rotamer: Outliers : 1.97 % Allowed : 7.04 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.93 (0.23), residues: 1068 helix: -0.38 (0.26), residues: 381 sheet: -0.12 (0.57), residues: 87 loop : -2.15 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP a 370 HIS 0.007 0.001 HIS a 305 PHE 0.018 0.002 PHE a 309 TYR 0.020 0.002 TYR c 419 ARG 0.006 0.001 ARG a 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00794 ( 33) link_NAG-ASN : angle 3.08734 ( 99) link_ALPHA1-6 : bond 0.00589 ( 9) link_ALPHA1-6 : angle 1.65140 ( 27) link_BETA1-4 : bond 0.01033 ( 36) link_BETA1-4 : angle 3.29399 ( 108) link_ALPHA1-3 : bond 0.00657 ( 9) link_ALPHA1-3 : angle 4.03839 ( 27) hydrogen bonds : bond 0.06308 ( 333) hydrogen bonds : angle 5.98048 ( 891) link_BETA1-6 : bond 0.01873 ( 3) link_BETA1-6 : angle 3.19589 ( 9) SS BOND : bond 0.00975 ( 21) SS BOND : angle 3.82144 ( 42) covalent geometry : bond 0.00551 ( 9993) covalent geometry : angle 1.03395 (13536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7081 (tmt) REVERT: a 359 MET cc_start: 0.8790 (tpp) cc_final: 0.8451 (mtp) REVERT: a 414 MET cc_start: 0.9316 (tmm) cc_final: 0.8843 (tmm) REVERT: B 82 MET cc_start: 0.8992 (pmm) cc_final: 0.8179 (pmm) REVERT: b 414 MET cc_start: 0.9283 (tmm) cc_final: 0.9056 (mtt) REVERT: C 82 MET cc_start: 0.9122 (pmm) cc_final: 0.8467 (pmm) REVERT: C 134 MET cc_start: 0.8771 (tpp) cc_final: 0.8428 (tpp) REVERT: C 194 MET cc_start: 0.9068 (tpt) cc_final: 0.8728 (tpp) REVERT: c 414 MET cc_start: 0.9274 (tmm) cc_final: 0.8743 (tmm) outliers start: 19 outliers final: 11 residues processed: 150 average time/residue: 0.2412 time to fit residues: 49.4315 Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 70 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.053691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.041964 restraints weight = 56520.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.043396 restraints weight = 32749.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.044334 restraints weight = 23555.327| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 10104 Z= 0.207 Angle : 0.977 10.781 13848 Z= 0.466 Chirality : 0.049 0.325 1755 Planarity : 0.004 0.029 1587 Dihedral : 13.554 85.713 2988 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.89 % Favored : 88.01 % Rotamer: Outliers : 2.38 % Allowed : 8.39 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.88 (0.24), residues: 1068 helix: -0.15 (0.28), residues: 378 sheet: -0.47 (0.58), residues: 87 loop : -2.18 (0.22), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 210 HIS 0.007 0.001 HIS B 131 PHE 0.014 0.001 PHE c 309 TYR 0.019 0.002 TYR C 150 ARG 0.008 0.001 ARG a 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 33) link_NAG-ASN : angle 2.36298 ( 99) link_ALPHA1-6 : bond 0.00599 ( 9) link_ALPHA1-6 : angle 1.87649 ( 27) link_BETA1-4 : bond 0.00728 ( 36) link_BETA1-4 : angle 2.56734 ( 108) link_ALPHA1-3 : bond 0.00772 ( 9) link_ALPHA1-3 : angle 3.64077 ( 27) hydrogen bonds : bond 0.05109 ( 333) hydrogen bonds : angle 5.78175 ( 891) link_BETA1-6 : bond 0.00720 ( 3) link_BETA1-6 : angle 3.53026 ( 9) SS BOND : bond 0.01069 ( 21) SS BOND : angle 3.64074 ( 42) covalent geometry : bond 0.00466 ( 9993) covalent geometry : angle 0.89425 (13536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.988 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 82 MET cc_start: 0.8960 (pmm) cc_final: 0.8331 (pmm) REVERT: A 134 MET cc_start: 0.7701 (ttp) cc_final: 0.7336 (tmm) REVERT: a 359 MET cc_start: 0.9056 (tpp) cc_final: 0.8702 (mmp) REVERT: B 82 MET cc_start: 0.8714 (pmm) cc_final: 0.8339 (pmm) REVERT: b 410 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7621 (ttm) REVERT: b 414 MET cc_start: 0.9318 (tmm) cc_final: 0.8786 (tmm) REVERT: C 82 MET cc_start: 0.9099 (pmm) cc_final: 0.8386 (pmm) REVERT: C 134 MET cc_start: 0.8724 (tpp) cc_final: 0.8404 (ttm) REVERT: C 194 MET cc_start: 0.9030 (tpt) cc_final: 0.8590 (tpp) REVERT: c 359 MET cc_start: 0.8371 (mmm) cc_final: 0.7905 (mtp) REVERT: c 414 MET cc_start: 0.9368 (tmm) cc_final: 0.8788 (tmm) REVERT: c 417 LYS cc_start: 0.9209 (tppt) cc_final: 0.8953 (ttmm) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 0.2364 time to fit residues: 43.6933 Evaluate side-chains 124 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain b residue 410 MET Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.053066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.041609 restraints weight = 55843.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.043025 restraints weight = 31789.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.043997 restraints weight = 22647.100| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10104 Z= 0.182 Angle : 0.867 8.076 13848 Z= 0.413 Chirality : 0.048 0.338 1755 Planarity : 0.004 0.030 1587 Dihedral : 11.987 80.881 2988 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.99 % Favored : 87.73 % Rotamer: Outliers : 2.59 % Allowed : 10.14 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.05 (0.24), residues: 1068 helix: -0.31 (0.27), residues: 396 sheet: -0.64 (0.57), residues: 87 loop : -2.31 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP c 370 HIS 0.004 0.001 HIS B 179 PHE 0.012 0.001 PHE b 309 TYR 0.015 0.002 TYR b 419 ARG 0.009 0.001 ARG c 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 33) link_NAG-ASN : angle 1.96640 ( 99) link_ALPHA1-6 : bond 0.00570 ( 9) link_ALPHA1-6 : angle 1.91231 ( 27) link_BETA1-4 : bond 0.00616 ( 36) link_BETA1-4 : angle 2.31498 ( 108) link_ALPHA1-3 : bond 0.00759 ( 9) link_ALPHA1-3 : angle 3.69558 ( 27) hydrogen bonds : bond 0.04674 ( 333) hydrogen bonds : angle 5.53331 ( 891) link_BETA1-6 : bond 0.00040 ( 3) link_BETA1-6 : angle 1.21164 ( 9) SS BOND : bond 0.00851 ( 21) SS BOND : angle 2.42160 ( 42) covalent geometry : bond 0.00405 ( 9993) covalent geometry : angle 0.80283 (13536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.979 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 82 MET cc_start: 0.8891 (pmm) cc_final: 0.8240 (pmm) REVERT: A 134 MET cc_start: 0.7907 (ttp) cc_final: 0.7461 (tmm) REVERT: a 359 MET cc_start: 0.9022 (tpp) cc_final: 0.8695 (mtp) REVERT: a 366 TYR cc_start: 0.7915 (m-10) cc_final: 0.7657 (m-10) REVERT: B 134 MET cc_start: 0.9067 (tpp) cc_final: 0.8341 (ttm) REVERT: b 414 MET cc_start: 0.9349 (tmm) cc_final: 0.8858 (tmm) REVERT: b 420 MET cc_start: 0.9279 (mmm) cc_final: 0.9062 (mmt) REVERT: C 82 MET cc_start: 0.9028 (pmm) cc_final: 0.8247 (pmm) REVERT: C 134 MET cc_start: 0.8576 (tpp) cc_final: 0.8373 (ttm) REVERT: C 194 MET cc_start: 0.9030 (tpt) cc_final: 0.8474 (tpp) REVERT: c 359 MET cc_start: 0.8519 (mmm) cc_final: 0.8199 (mtp) REVERT: c 366 TYR cc_start: 0.8027 (m-80) cc_final: 0.7622 (m-10) REVERT: c 414 MET cc_start: 0.9353 (tmm) cc_final: 0.8902 (tmm) outliers start: 25 outliers final: 12 residues processed: 132 average time/residue: 0.2098 time to fit residues: 39.1958 Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 0.0070 chunk 52 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 overall best weight: 2.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN C 124 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.052613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.040817 restraints weight = 57098.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.042163 restraints weight = 34148.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.043106 restraints weight = 24846.780| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10104 Z= 0.204 Angle : 0.910 11.545 13848 Z= 0.430 Chirality : 0.050 0.335 1755 Planarity : 0.004 0.031 1587 Dihedral : 11.284 77.850 2988 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.64 % Favored : 86.89 % Rotamer: Outliers : 2.69 % Allowed : 11.90 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -2.39 (0.24), residues: 1068 helix: -0.63 (0.26), residues: 423 sheet: -0.56 (0.53), residues: 105 loop : -2.67 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 210 HIS 0.010 0.001 HIS C 124 PHE 0.013 0.001 PHE b 309 TYR 0.016 0.002 TYR A 150 ARG 0.004 0.001 ARG a 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 33) link_NAG-ASN : angle 2.07750 ( 99) link_ALPHA1-6 : bond 0.00575 ( 9) link_ALPHA1-6 : angle 1.92044 ( 27) link_BETA1-4 : bond 0.00594 ( 36) link_BETA1-4 : angle 2.19991 ( 108) link_ALPHA1-3 : bond 0.00798 ( 9) link_ALPHA1-3 : angle 3.57817 ( 27) hydrogen bonds : bond 0.04647 ( 333) hydrogen bonds : angle 5.52962 ( 891) link_BETA1-6 : bond 0.00110 ( 3) link_BETA1-6 : angle 1.94566 ( 9) SS BOND : bond 0.00896 ( 21) SS BOND : angle 2.24486 ( 42) covalent geometry : bond 0.00447 ( 9993) covalent geometry : angle 0.85157 (13536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8919 (pmm) cc_final: 0.8365 (pmm) REVERT: A 134 MET cc_start: 0.8139 (ttp) cc_final: 0.7821 (tmm) REVERT: A 194 MET cc_start: 0.9227 (tpt) cc_final: 0.8806 (tpp) REVERT: a 351 MET cc_start: 0.9233 (mmm) cc_final: 0.8759 (mmm) REVERT: a 414 MET cc_start: 0.9326 (tmm) cc_final: 0.8818 (tmm) REVERT: B 82 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7732 (pmm) REVERT: b 308 GLU cc_start: 0.9182 (mp0) cc_final: 0.8584 (mt-10) REVERT: b 414 MET cc_start: 0.9389 (tmm) cc_final: 0.8961 (tmm) REVERT: C 82 MET cc_start: 0.9011 (pmm) cc_final: 0.8393 (pmm) REVERT: C 194 MET cc_start: 0.9085 (tpt) cc_final: 0.8717 (tpp) REVERT: C 210 TRP cc_start: 0.5991 (t-100) cc_final: 0.5731 (t-100) REVERT: c 351 MET cc_start: 0.9328 (mmm) cc_final: 0.8772 (mmm) REVERT: c 414 MET cc_start: 0.9394 (tmm) cc_final: 0.8999 (tmm) outliers start: 26 outliers final: 17 residues processed: 124 average time/residue: 0.2002 time to fit residues: 35.7375 Evaluate side-chains 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 87 optimal weight: 0.0470 chunk 98 optimal weight: 3.9990 overall best weight: 1.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN b 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.052892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.041290 restraints weight = 56192.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.042633 restraints weight = 33129.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.043570 restraints weight = 24086.796| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10104 Z= 0.170 Angle : 0.857 9.303 13848 Z= 0.403 Chirality : 0.049 0.352 1755 Planarity : 0.004 0.046 1587 Dihedral : 10.536 74.287 2988 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.20 % Favored : 86.24 % Rotamer: Outliers : 1.97 % Allowed : 13.98 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -2.22 (0.24), residues: 1068 helix: -0.45 (0.27), residues: 393 sheet: 0.97 (0.65), residues: 57 loop : -2.54 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 210 HIS 0.009 0.001 HIS C 124 PHE 0.013 0.001 PHE b 309 TYR 0.022 0.001 TYR A 150 ARG 0.004 0.001 ARG a 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 33) link_NAG-ASN : angle 1.94895 ( 99) link_ALPHA1-6 : bond 0.00611 ( 9) link_ALPHA1-6 : angle 1.88223 ( 27) link_BETA1-4 : bond 0.00542 ( 36) link_BETA1-4 : angle 2.09858 ( 108) link_ALPHA1-3 : bond 0.00744 ( 9) link_ALPHA1-3 : angle 3.67213 ( 27) hydrogen bonds : bond 0.04491 ( 333) hydrogen bonds : angle 5.36133 ( 891) link_BETA1-6 : bond 0.00056 ( 3) link_BETA1-6 : angle 1.78125 ( 9) SS BOND : bond 0.00677 ( 21) SS BOND : angle 2.16860 ( 42) covalent geometry : bond 0.00376 ( 9993) covalent geometry : angle 0.79808 (13536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8840 (pmm) cc_final: 0.8421 (pmm) REVERT: A 134 MET cc_start: 0.8251 (ttp) cc_final: 0.7821 (tmm) REVERT: A 194 MET cc_start: 0.9173 (tpt) cc_final: 0.8785 (tpp) REVERT: a 320 LYS cc_start: 0.9480 (tptp) cc_final: 0.9121 (tptp) REVERT: a 414 MET cc_start: 0.9321 (tmm) cc_final: 0.8849 (tmm) REVERT: B 82 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7816 (pmm) REVERT: B 134 MET cc_start: 0.9067 (tpp) cc_final: 0.8428 (ttm) REVERT: B 203 LEU cc_start: 0.7636 (mt) cc_final: 0.7382 (tt) REVERT: b 414 MET cc_start: 0.9383 (tmm) cc_final: 0.8998 (tmm) REVERT: C 82 MET cc_start: 0.8950 (pmm) cc_final: 0.8367 (pmm) REVERT: C 153 MET cc_start: 0.6689 (mpp) cc_final: 0.6442 (mpp) REVERT: C 194 MET cc_start: 0.9114 (tpt) cc_final: 0.8745 (tpp) REVERT: c 414 MET cc_start: 0.9399 (tmm) cc_final: 0.9025 (tmm) REVERT: c 417 LYS cc_start: 0.9219 (tppt) cc_final: 0.8866 (ttmm) outliers start: 19 outliers final: 11 residues processed: 126 average time/residue: 0.2222 time to fit residues: 39.2237 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 55 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.053096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.041258 restraints weight = 56617.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.042618 restraints weight = 33933.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.043546 restraints weight = 24684.025| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 10104 Z= 0.172 Angle : 0.865 10.116 13848 Z= 0.407 Chirality : 0.049 0.347 1755 Planarity : 0.004 0.044 1587 Dihedral : 10.179 72.378 2988 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.64 % Favored : 86.80 % Rotamer: Outliers : 1.76 % Allowed : 15.22 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -2.16 (0.24), residues: 1068 helix: -0.45 (0.27), residues: 396 sheet: 0.85 (0.58), residues: 75 loop : -2.57 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 210 HIS 0.006 0.001 HIS c 305 PHE 0.009 0.001 PHE c 309 TYR 0.018 0.001 TYR A 150 ARG 0.008 0.001 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 33) link_NAG-ASN : angle 1.91200 ( 99) link_ALPHA1-6 : bond 0.00608 ( 9) link_ALPHA1-6 : angle 1.85223 ( 27) link_BETA1-4 : bond 0.00536 ( 36) link_BETA1-4 : angle 2.08411 ( 108) link_ALPHA1-3 : bond 0.00715 ( 9) link_ALPHA1-3 : angle 3.58343 ( 27) hydrogen bonds : bond 0.04370 ( 333) hydrogen bonds : angle 5.33182 ( 891) link_BETA1-6 : bond 0.00047 ( 3) link_BETA1-6 : angle 1.85278 ( 9) SS BOND : bond 0.01040 ( 21) SS BOND : angle 2.41463 ( 42) covalent geometry : bond 0.00387 ( 9993) covalent geometry : angle 0.80741 (13536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8346 (ttp) cc_final: 0.8012 (tmm) REVERT: a 311 ASP cc_start: 0.9170 (m-30) cc_final: 0.8740 (m-30) REVERT: a 320 LYS cc_start: 0.9493 (tptp) cc_final: 0.9139 (tptp) REVERT: a 414 MET cc_start: 0.9339 (tmm) cc_final: 0.8921 (tmm) REVERT: B 82 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7765 (pmm) REVERT: B 134 MET cc_start: 0.9049 (tpp) cc_final: 0.8498 (ttm) REVERT: B 203 LEU cc_start: 0.7732 (mt) cc_final: 0.7476 (tt) REVERT: b 414 MET cc_start: 0.9382 (tmm) cc_final: 0.9008 (tmm) REVERT: C 82 MET cc_start: 0.8971 (pmm) cc_final: 0.8733 (pmm) REVERT: C 134 MET cc_start: 0.8309 (ttm) cc_final: 0.7643 (tmm) REVERT: C 153 MET cc_start: 0.6684 (mpp) cc_final: 0.6424 (mpp) REVERT: C 194 MET cc_start: 0.9091 (tpt) cc_final: 0.8663 (tpp) REVERT: C 210 TRP cc_start: 0.5725 (t-100) cc_final: 0.5510 (t-100) REVERT: c 311 ASP cc_start: 0.9206 (m-30) cc_final: 0.8590 (m-30) REVERT: c 351 MET cc_start: 0.9266 (mmm) cc_final: 0.8743 (mmm) REVERT: c 414 MET cc_start: 0.9419 (tmm) cc_final: 0.8859 (tmm) outliers start: 17 outliers final: 14 residues processed: 116 average time/residue: 0.2070 time to fit residues: 34.7120 Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 0.0070 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.053362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.041686 restraints weight = 56241.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.043058 restraints weight = 33313.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.043985 restraints weight = 24051.985| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10104 Z= 0.158 Angle : 0.842 10.425 13848 Z= 0.397 Chirality : 0.048 0.350 1755 Planarity : 0.004 0.039 1587 Dihedral : 9.731 69.473 2988 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.58 % Favored : 85.86 % Rotamer: Outliers : 2.28 % Allowed : 15.32 % Favored : 82.40 % 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: -2.10 (0.24), residues: 1068 helix: -0.10 (0.27), residues: 381 sheet: 0.56 (0.63), residues: 57 loop : -2.57 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 210 HIS 0.004 0.001 HIS a 305 PHE 0.011 0.001 PHE a 309 TYR 0.015 0.001 TYR A 150 ARG 0.007 0.001 ARG A 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 33) link_NAG-ASN : angle 1.84189 ( 99) link_ALPHA1-6 : bond 0.00613 ( 9) link_ALPHA1-6 : angle 1.80498 ( 27) link_BETA1-4 : bond 0.00534 ( 36) link_BETA1-4 : angle 2.05905 ( 108) link_ALPHA1-3 : bond 0.00661 ( 9) link_ALPHA1-3 : angle 3.54257 ( 27) hydrogen bonds : bond 0.04093 ( 333) hydrogen bonds : angle 5.26244 ( 891) link_BETA1-6 : bond 0.00089 ( 3) link_BETA1-6 : angle 1.80027 ( 9) SS BOND : bond 0.00774 ( 21) SS BOND : angle 2.10120 ( 42) covalent geometry : bond 0.00354 ( 9993) covalent geometry : angle 0.78748 (13536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8323 (ttp) cc_final: 0.7901 (tmm) REVERT: A 192 MET cc_start: 0.8127 (mpp) cc_final: 0.7905 (mpp) REVERT: a 311 ASP cc_start: 0.9172 (m-30) cc_final: 0.8757 (m-30) REVERT: a 332 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.7987 (mtp) REVERT: a 414 MET cc_start: 0.9332 (tmm) cc_final: 0.8924 (tmm) REVERT: B 82 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7538 (pmm) REVERT: B 134 MET cc_start: 0.9037 (tpp) cc_final: 0.8533 (ttm) REVERT: B 153 MET cc_start: 0.6334 (mpp) cc_final: 0.5948 (mpp) REVERT: B 203 LEU cc_start: 0.7652 (mt) cc_final: 0.7438 (tt) REVERT: b 311 ASP cc_start: 0.9299 (m-30) cc_final: 0.8609 (m-30) REVERT: b 332 MET cc_start: 0.8859 (tpp) cc_final: 0.8493 (tpp) REVERT: b 399 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8362 (t80) REVERT: b 414 MET cc_start: 0.9379 (tmm) cc_final: 0.8899 (tmm) REVERT: C 80 MET cc_start: 0.9279 (tpp) cc_final: 0.9076 (tpp) REVERT: C 82 MET cc_start: 0.8915 (pmm) cc_final: 0.8322 (pmm) REVERT: C 134 MET cc_start: 0.8381 (ttm) cc_final: 0.7673 (tmm) REVERT: C 153 MET cc_start: 0.6696 (mpp) cc_final: 0.6440 (mpp) REVERT: C 194 MET cc_start: 0.9061 (tpt) cc_final: 0.8643 (tpp) REVERT: c 311 ASP cc_start: 0.9213 (m-30) cc_final: 0.8589 (m-30) REVERT: c 414 MET cc_start: 0.9433 (tmm) cc_final: 0.8912 (tmm) REVERT: c 417 LYS cc_start: 0.9224 (tppt) cc_final: 0.8907 (ttmm) outliers start: 22 outliers final: 14 residues processed: 124 average time/residue: 0.2149 time to fit residues: 37.7598 Evaluate side-chains 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 399 PHE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** b 405 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 = 0.3446 r_free = 0.3446 target = 0.052298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.040893 restraints weight = 57226.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.042239 restraints weight = 32777.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.043160 restraints weight = 23480.457| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10104 Z= 0.199 Angle : 0.884 10.375 13848 Z= 0.417 Chirality : 0.048 0.337 1755 Planarity : 0.004 0.047 1587 Dihedral : 9.713 68.391 2988 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.39 % Favored : 86.05 % Rotamer: Outliers : 2.07 % Allowed : 15.42 % Favored : 82.51 % 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: -2.05 (0.25), residues: 1068 helix: -0.15 (0.27), residues: 387 sheet: 0.48 (0.58), residues: 75 loop : -2.57 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP C 210 HIS 0.004 0.001 HIS C 124 PHE 0.013 0.001 PHE b 309 TYR 0.014 0.002 TYR A 217 ARG 0.018 0.001 ARG b 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 33) link_NAG-ASN : angle 1.92791 ( 99) link_ALPHA1-6 : bond 0.00572 ( 9) link_ALPHA1-6 : angle 1.77599 ( 27) link_BETA1-4 : bond 0.00499 ( 36) link_BETA1-4 : angle 2.07344 ( 108) link_ALPHA1-3 : bond 0.00659 ( 9) link_ALPHA1-3 : angle 3.37192 ( 27) hydrogen bonds : bond 0.04253 ( 333) hydrogen bonds : angle 5.44668 ( 891) link_BETA1-6 : bond 0.00229 ( 3) link_BETA1-6 : angle 2.05327 ( 9) SS BOND : bond 0.00748 ( 21) SS BOND : angle 2.02653 ( 42) covalent geometry : bond 0.00444 ( 9993) covalent geometry : angle 0.83304 (13536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8326 (ttp) cc_final: 0.7922 (tmm) REVERT: A 192 MET cc_start: 0.8179 (mpp) cc_final: 0.7880 (mpp) REVERT: a 311 ASP cc_start: 0.9126 (m-30) cc_final: 0.8700 (m-30) REVERT: a 332 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8085 (mtp) REVERT: a 414 MET cc_start: 0.9347 (tmm) cc_final: 0.8955 (tmm) REVERT: B 82 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7473 (pmm) REVERT: B 125 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9143 (pptt) REVERT: B 134 MET cc_start: 0.9042 (tpp) cc_final: 0.8555 (ttm) REVERT: B 203 LEU cc_start: 0.7658 (mt) cc_final: 0.7420 (tt) REVERT: b 332 MET cc_start: 0.8961 (tpp) cc_final: 0.8569 (tpp) REVERT: b 399 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8385 (t80) REVERT: b 413 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8565 (tm-30) REVERT: b 414 MET cc_start: 0.9381 (tmm) cc_final: 0.8960 (tmm) REVERT: b 417 LYS cc_start: 0.9305 (tppt) cc_final: 0.8966 (ttmt) REVERT: C 82 MET cc_start: 0.8969 (pmm) cc_final: 0.8623 (pmm) REVERT: C 134 MET cc_start: 0.8374 (ttm) cc_final: 0.7650 (tmm) REVERT: C 194 MET cc_start: 0.9143 (tpt) cc_final: 0.8759 (tpp) REVERT: c 311 ASP cc_start: 0.9222 (m-30) cc_final: 0.8620 (m-30) REVERT: c 414 MET cc_start: 0.9407 (tmm) cc_final: 0.8910 (tmm) REVERT: c 417 LYS cc_start: 0.9208 (tppt) cc_final: 0.8868 (ttmm) outliers start: 20 outliers final: 13 residues processed: 112 average time/residue: 0.2076 time to fit residues: 33.7520 Evaluate side-chains 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain a residue 332 MET Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 399 PHE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** b 405 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 = 0.3438 r_free = 0.3438 target = 0.052191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040775 restraints weight = 56711.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.042113 restraints weight = 32502.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.043021 restraints weight = 23293.115| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10104 Z= 0.208 Angle : 0.896 10.970 13848 Z= 0.423 Chirality : 0.049 0.342 1755 Planarity : 0.004 0.050 1587 Dihedral : 9.656 66.522 2988 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.01 % Favored : 86.42 % Rotamer: Outliers : 1.76 % Allowed : 15.94 % Favored : 82.30 % 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: -2.28 (0.24), residues: 1068 helix: -0.45 (0.26), residues: 408 sheet: 0.25 (0.58), residues: 75 loop : -2.67 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A 210 HIS 0.004 0.001 HIS C 124 PHE 0.010 0.001 PHE c 309 TYR 0.021 0.002 TYR b 371 ARG 0.014 0.001 ARG b 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 33) link_NAG-ASN : angle 1.97889 ( 99) link_ALPHA1-6 : bond 0.00570 ( 9) link_ALPHA1-6 : angle 1.74248 ( 27) link_BETA1-4 : bond 0.00493 ( 36) link_BETA1-4 : angle 2.07200 ( 108) link_ALPHA1-3 : bond 0.00631 ( 9) link_ALPHA1-3 : angle 3.37565 ( 27) hydrogen bonds : bond 0.04278 ( 333) hydrogen bonds : angle 5.50684 ( 891) link_BETA1-6 : bond 0.00211 ( 3) link_BETA1-6 : angle 2.16921 ( 9) SS BOND : bond 0.00789 ( 21) SS BOND : angle 2.03765 ( 42) covalent geometry : bond 0.00465 ( 9993) covalent geometry : angle 0.84519 (13536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8467 (ttp) cc_final: 0.8085 (tmm) REVERT: a 311 ASP cc_start: 0.9173 (m-30) cc_final: 0.8741 (m-30) REVERT: a 414 MET cc_start: 0.9339 (tmm) cc_final: 0.8961 (tmm) REVERT: B 82 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7521 (pmm) REVERT: B 125 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9170 (pptt) REVERT: B 134 MET cc_start: 0.8999 (tpp) cc_final: 0.8488 (ttm) REVERT: B 153 MET cc_start: 0.6463 (mpp) cc_final: 0.6185 (mpp) REVERT: B 203 LEU cc_start: 0.7679 (mt) cc_final: 0.7448 (tt) REVERT: b 311 ASP cc_start: 0.9321 (m-30) cc_final: 0.8588 (m-30) REVERT: b 332 MET cc_start: 0.8912 (tpp) cc_final: 0.8571 (tpp) REVERT: b 399 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8418 (t80) REVERT: b 414 MET cc_start: 0.9403 (tmm) cc_final: 0.9033 (tmm) REVERT: C 82 MET cc_start: 0.8770 (pmm) cc_final: 0.8331 (pmm) REVERT: C 134 MET cc_start: 0.8384 (ttm) cc_final: 0.7611 (tmm) REVERT: C 194 MET cc_start: 0.9154 (tpt) cc_final: 0.8777 (tpp) REVERT: c 311 ASP cc_start: 0.9222 (m-30) cc_final: 0.8621 (m-30) REVERT: c 414 MET cc_start: 0.9437 (tmm) cc_final: 0.8949 (tmm) outliers start: 17 outliers final: 11 residues processed: 104 average time/residue: 0.1970 time to fit residues: 30.1668 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 399 PHE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 405 GLN C 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.052859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041178 restraints weight = 56769.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.042563 restraints weight = 33129.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.043486 restraints weight = 23836.388| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10104 Z= 0.167 Angle : 0.866 10.989 13848 Z= 0.408 Chirality : 0.048 0.350 1755 Planarity : 0.004 0.042 1587 Dihedral : 9.375 63.912 2988 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.20 % Favored : 86.24 % Rotamer: Outliers : 1.66 % Allowed : 16.46 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.13 (0.25), residues: 1068 helix: -0.13 (0.27), residues: 390 sheet: 0.18 (0.58), residues: 75 loop : -2.66 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 210 HIS 0.004 0.001 HIS C 124 PHE 0.009 0.001 PHE C 233 TYR 0.015 0.001 TYR b 419 ARG 0.015 0.001 ARG b 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 33) link_NAG-ASN : angle 1.87587 ( 99) link_ALPHA1-6 : bond 0.00621 ( 9) link_ALPHA1-6 : angle 1.69768 ( 27) link_BETA1-4 : bond 0.00510 ( 36) link_BETA1-4 : angle 2.05504 ( 108) link_ALPHA1-3 : bond 0.00599 ( 9) link_ALPHA1-3 : angle 3.42520 ( 27) hydrogen bonds : bond 0.04149 ( 333) hydrogen bonds : angle 5.42378 ( 891) link_BETA1-6 : bond 0.00032 ( 3) link_BETA1-6 : angle 1.96389 ( 9) SS BOND : bond 0.00672 ( 21) SS BOND : angle 1.96737 ( 42) covalent geometry : bond 0.00379 ( 9993) covalent geometry : angle 0.81471 (13536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2678.85 seconds wall clock time: 48 minutes 23.77 seconds (2903.77 seconds total)