Starting phenix.real_space_refine on Thu Jul 2 19:39:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ejf_28180/07_2026/8ejf_28180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejf_28180/07_2026/8ejf_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ejf_28180/07_2026/8ejf_28180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejf_28180/07_2026/8ejf_28180.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ejf_28180/07_2026/8ejf_28180.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ejf_28180/07_2026/8ejf_28180.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ejf_28180/07_2026/8ejf_28180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejf_28180/07_2026/8ejf_28180.map" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 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 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 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 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 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 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 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 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 chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 1.61, per 1000 atoms: 0.16 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: 1.16 Conformation dependent library (CDL) restraints added in 231.1 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: 0.14 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: 1.12 Time building geometry restraints manager: 1.43 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 - 14.60: 4978 14.60 - 29.21: 245 29.21 - 43.81: 39 43.81 - 58.41: 18 58.41 - 73.01: 24 Dihedral angle restraints: 5304 sinusoidal: 2133 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 5301 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: 0.02 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.690 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 10.607 69.359 3201 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (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 ARG 0.007 0.001 ARG c 314 TYR 0.088 0.011 TYR C 166 PHE 0.018 0.006 PHE c 309 TRP 0.032 0.008 TRP B 210 HIS 0.011 0.003 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.02407 / 1.27 ( 9993) covalent geometry : angle 1.99469 / 1.26 (13536) SS BOND : bond 0.08596 / 6.20 ( 21) SS BOND : angle 3.06833 / 1.91 ( 42) hydrogen bonds : bond 0.17340 / 11.35 ( 333) hydrogen bonds : angle 7.75561 / 5.44 ( 891) link_ALPHA1-3 : bond 0.09424 / 5.71 ( 9) link_ALPHA1-3 : angle 7.21873 / 3.63 ( 27) link_ALPHA1-6 : bond 0.05090 / 3.06 ( 9) link_ALPHA1-6 : angle 2.42488 / 1.23 ( 27) link_BETA1-4 : bond 0.07316 / 4.24 ( 36) link_BETA1-4 : angle 5.29219 / 3.41 ( 108) link_BETA1-6 : bond 0.08822 / 4.42 ( 3) link_BETA1-6 : angle 7.74284 / 3.78 ( 9) link_NAG-ASN : bond 0.07677 / 4.42 ( 33) link_NAG-ASN : angle 3.91803 / 2.24 ( 99) *********************** 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 : 0.222 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: 0.7710 (tpp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1117 time to fit residues: 32.5434 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 : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3510 r_free = 0.3510 target = 0.054696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.043096 restraints weight = 55422.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.044506 restraints weight = 31611.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.045455 restraints weight = 22570.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.046115 restraints weight = 18256.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.046565 restraints weight = 15789.519| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 10104 Z= 0.243 Angle : 1.108 10.891 13848 Z= 0.532 Chirality : 0.049 0.212 1755 Planarity : 0.005 0.033 1587 Dihedral : 6.845 39.719 1170 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.58 % Favored : 89.33 % Rotamer: Outliers : 1.86 % Allowed : 7.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.23), residues: 1068 helix: -0.63 (0.25), residues: 399 sheet: -0.08 (0.58), residues: 87 loop : -2.14 (0.21), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 325 TYR 0.019 0.003 TYR c 419 PHE 0.018 0.002 PHE a 309 TRP 0.020 0.003 TRP a 370 HIS 0.008 0.001 HIS a 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 ( 9993) covalent geometry : angle 1.02411 / 0.51 (13536) SS BOND : bond 0.00686 / 0.44 ( 21) SS BOND : angle 3.71232 / 2.23 ( 42) hydrogen bonds : bond 0.06103 / 3.98 ( 333) hydrogen bonds : angle 5.97327 / 4.26 ( 891) link_ALPHA1-3 : bond 0.00644 / 0.41 ( 9) link_ALPHA1-3 : angle 3.16322 / 1.66 ( 27) link_ALPHA1-6 : bond 0.00386 / 0.23 ( 9) link_ALPHA1-6 : angle 1.58535 / 1.02 ( 27) link_BETA1-4 : bond 0.00885 / 0.52 ( 36) link_BETA1-4 : angle 2.96669 / 2.00 ( 108) link_BETA1-6 : bond 0.00975 / 0.49 ( 3) link_BETA1-6 : angle 2.56268 / 1.40 ( 9) link_NAG-ASN : bond 0.00668 / 0.42 ( 33) link_NAG-ASN : angle 2.97254 / 1.76 ( 99) *********************** 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 155 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.366 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: A 134 MET cc_start: 0.7519 (ttp) cc_final: 0.7163 (tmt) REVERT: A 194 MET cc_start: 0.9097 (tpt) cc_final: 0.8667 (tpp) REVERT: a 359 MET cc_start: 0.8772 (tpp) cc_final: 0.8433 (mtp) REVERT: a 399 PHE cc_start: 0.8430 (t80) cc_final: 0.7667 (t80) REVERT: B 82 MET cc_start: 0.8911 (pmm) cc_final: 0.8148 (pmm) REVERT: B 210 TRP cc_start: 0.5632 (t-100) cc_final: 0.5225 (t-100) REVERT: b 414 MET cc_start: 0.9274 (tmm) cc_final: 0.8964 (mtt) REVERT: C 82 MET cc_start: 0.9077 (pmm) cc_final: 0.8399 (pmm) REVERT: C 134 MET cc_start: 0.8790 (tpp) cc_final: 0.8447 (tpp) REVERT: C 194 MET cc_start: 0.9075 (tpt) cc_final: 0.8738 (tpp) REVERT: c 399 PHE cc_start: 0.8133 (t80) cc_final: 0.7456 (t80) REVERT: c 414 MET cc_start: 0.9235 (tmm) cc_final: 0.8698 (tmm) outliers start: 18 outliers final: 12 residues processed: 152 average time/residue: 0.1085 time to fit residues: 22.7546 Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 253 TYR 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 49 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.052670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.040797 restraints weight = 57296.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.042164 restraints weight = 33984.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.043078 restraints weight = 24779.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.043702 restraints weight = 20278.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.043990 restraints weight = 17763.315| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 10104 Z= 0.245 Angle : 0.995 11.106 13848 Z= 0.479 Chirality : 0.047 0.216 1755 Planarity : 0.004 0.027 1587 Dihedral : 6.709 39.230 1170 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.99 % Favored : 87.92 % Rotamer: Outliers : 2.48 % Allowed : 8.39 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.24), residues: 1068 helix: -0.24 (0.27), residues: 384 sheet: -0.61 (0.58), residues: 87 loop : -2.25 (0.21), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 422 TYR 0.018 0.002 TYR C 150 PHE 0.015 0.002 PHE c 309 TRP 0.013 0.002 TRP A 210 HIS 0.005 0.001 HIS a 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 ( 9993) covalent geometry : angle 0.92854 / 0.46 (13536) SS BOND : bond 0.00773 / 0.47 ( 21) SS BOND : angle 3.52711 / 2.10 ( 42) hydrogen bonds : bond 0.05205 / 3.42 ( 333) hydrogen bonds : angle 5.92709 / 4.17 ( 891) link_ALPHA1-3 : bond 0.00533 / 0.32 ( 9) link_ALPHA1-3 : angle 3.10224 / 1.63 ( 27) link_ALPHA1-6 : bond 0.00269 / 0.15 ( 9) link_ALPHA1-6 : angle 1.59275 / 1.03 ( 27) link_BETA1-4 : bond 0.00648 / 0.37 ( 36) link_BETA1-4 : angle 2.24792 / 1.50 ( 108) link_BETA1-6 : bond 0.00986 / 0.49 ( 3) link_BETA1-6 : angle 2.98158 / 1.63 ( 9) link_NAG-ASN : bond 0.00338 / 0.22 ( 33) link_NAG-ASN : angle 2.39324 / 1.48 ( 99) *********************** 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 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.367 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: 0.8939 (pmm) cc_final: 0.8390 (pmm) REVERT: A 134 MET cc_start: 0.7809 (ttp) cc_final: 0.7430 (tmm) REVERT: B 82 MET cc_start: 0.8741 (pmm) cc_final: 0.8339 (pmm) REVERT: b 410 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7625 (ttm) REVERT: b 414 MET cc_start: 0.9327 (tmm) cc_final: 0.8787 (tmm) REVERT: C 82 MET cc_start: 0.9122 (pmm) cc_final: 0.8386 (pmm) REVERT: C 134 MET cc_start: 0.8719 (tpp) cc_final: 0.8373 (tpp) REVERT: C 194 MET cc_start: 0.9098 (tpt) cc_final: 0.8687 (tpp) REVERT: c 359 MET cc_start: 0.8415 (mmm) cc_final: 0.7945 (mtp) REVERT: c 414 MET cc_start: 0.9337 (tmm) cc_final: 0.8834 (tmm) REVERT: c 417 LYS cc_start: 0.9210 (tppt) cc_final: 0.8969 (ttmm) outliers start: 24 outliers final: 20 residues processed: 132 average time/residue: 0.0938 time to fit residues: 17.6008 Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain a residue 398 HIS Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS 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 266 LEU 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 20 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 26 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 ASN B 124 HIS b 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.052474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.040672 restraints weight = 57747.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.042034 restraints weight = 34027.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.043005 restraints weight = 24887.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.043566 restraints weight = 20330.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.043996 restraints weight = 18004.126| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10104 Z= 0.202 Angle : 0.893 9.086 13848 Z= 0.427 Chirality : 0.045 0.209 1755 Planarity : 0.004 0.030 1587 Dihedral : 6.327 34.546 1170 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.83 % Favored : 87.08 % Rotamer: Outliers : 3.31 % Allowed : 9.11 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.24), residues: 1068 helix: -0.35 (0.27), residues: 384 sheet: -0.88 (0.56), residues: 87 loop : -2.35 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 422 TYR 0.016 0.002 TYR b 419 PHE 0.013 0.001 PHE c 399 TRP 0.018 0.002 TRP A 210 HIS 0.010 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 ( 9993) covalent geometry : angle 0.84182 / 0.42 (13536) SS BOND : bond 0.00603 / 0.36 ( 21) SS BOND : angle 2.46438 / 1.43 ( 42) hydrogen bonds : bond 0.04746 / 3.11 ( 333) hydrogen bonds : angle 5.72609 / 4.01 ( 891) link_ALPHA1-3 : bond 0.00542 / 0.33 ( 9) link_ALPHA1-3 : angle 2.94271 / 1.57 ( 27) link_ALPHA1-6 : bond 0.00273 / 0.15 ( 9) link_ALPHA1-6 : angle 1.63275 / 1.05 ( 27) link_BETA1-4 : bond 0.00539 / 0.31 ( 36) link_BETA1-4 : angle 1.94822 / 1.32 ( 108) link_BETA1-6 : bond 0.00590 / 0.30 ( 3) link_BETA1-6 : angle 2.77551 / 1.54 ( 9) link_NAG-ASN : bond 0.00292 / 0.19 ( 33) link_NAG-ASN : angle 2.01205 / 1.28 ( 99) *********************** 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 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.360 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 82 MET cc_start: 0.8782 (pmm) cc_final: 0.8210 (pmm) REVERT: A 134 MET cc_start: 0.7985 (ttp) cc_final: 0.7571 (tmm) REVERT: A 194 MET cc_start: 0.9226 (tpt) cc_final: 0.8794 (tpp) REVERT: a 359 MET cc_start: 0.9001 (tpp) cc_final: 0.8621 (mtp) REVERT: a 381 SER cc_start: 0.8093 (p) cc_final: 0.7831 (p) REVERT: a 414 MET cc_start: 0.9300 (tmm) cc_final: 0.8736 (tmm) REVERT: B 134 MET cc_start: 0.8494 (tpp) cc_final: 0.8288 (ttm) REVERT: b 414 MET cc_start: 0.9345 (tmm) cc_final: 0.8830 (tmm) REVERT: C 82 MET cc_start: 0.9061 (pmm) cc_final: 0.8266 (pmm) REVERT: C 194 MET cc_start: 0.9078 (tpt) cc_final: 0.8567 (tpp) REVERT: C 210 TRP cc_start: 0.6282 (t-100) cc_final: 0.5837 (t-100) REVERT: c 359 MET cc_start: 0.8581 (mmm) cc_final: 0.8261 (mtp) REVERT: c 414 MET cc_start: 0.9340 (tmm) cc_final: 0.8827 (tmm) outliers start: 32 outliers final: 16 residues processed: 137 average time/residue: 0.0954 time to fit residues: 18.5578 Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain a residue 347 ASP 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 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 192 MET 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 Chi-restraints excluded: chain c residue 402 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 149 GLN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.051577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.039767 restraints weight = 58139.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.041083 restraints weight = 34878.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.041976 restraints weight = 25560.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.042598 restraints weight = 21009.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.043033 restraints weight = 18445.398| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10104 Z= 0.236 Angle : 0.916 10.879 13848 Z= 0.438 Chirality : 0.046 0.213 1755 Planarity : 0.004 0.045 1587 Dihedral : 6.558 33.731 1170 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.92 % Favored : 86.61 % Rotamer: Outliers : 3.00 % Allowed : 11.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.24), residues: 1068 helix: -0.40 (0.27), residues: 387 sheet: -1.09 (0.57), residues: 87 loop : -2.46 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 422 TYR 0.021 0.002 TYR A 150 PHE 0.016 0.002 PHE b 309 TRP 0.011 0.002 TRP A 196 HIS 0.005 0.001 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 ( 9993) covalent geometry : angle 0.87261 / 0.43 (13536) SS BOND : bond 0.00813 / 0.49 ( 21) SS BOND : angle 1.89240 / 1.16 ( 42) hydrogen bonds : bond 0.04756 / 3.07 ( 333) hydrogen bonds : angle 5.59760 / 3.91 ( 891) link_ALPHA1-3 : bond 0.00483 / 0.29 ( 9) link_ALPHA1-3 : angle 2.83731 / 1.54 ( 27) link_ALPHA1-6 : bond 0.00219 / 0.12 ( 9) link_ALPHA1-6 : angle 1.71968 / 1.09 ( 27) link_BETA1-4 : bond 0.00513 / 0.29 ( 36) link_BETA1-4 : angle 1.85350 / 1.24 ( 108) link_BETA1-6 : bond 0.00088 / 0.05 ( 3) link_BETA1-6 : angle 2.28430 / 1.22 ( 9) link_NAG-ASN : bond 0.00237 / 0.13 ( 33) link_NAG-ASN : angle 2.09559 / 1.33 ( 99) *********************** 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 133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.310 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: 0.8226 (ttp) cc_final: 0.7887 (tmm) REVERT: A 194 MET cc_start: 0.9206 (tpt) cc_final: 0.8754 (tpp) REVERT: a 414 MET cc_start: 0.9371 (tmm) cc_final: 0.8889 (tmm) REVERT: B 82 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7785 (pmm) REVERT: B 153 MET cc_start: 0.6369 (mpp) cc_final: 0.6012 (mpp) REVERT: b 414 MET cc_start: 0.9372 (tmm) cc_final: 0.8925 (tmm) REVERT: C 153 MET cc_start: 0.6598 (mpp) cc_final: 0.6340 (mpp) REVERT: C 194 MET cc_start: 0.9191 (tpt) cc_final: 0.8807 (tpp) REVERT: C 210 TRP cc_start: 0.6436 (t-100) cc_final: 0.6088 (t-100) REVERT: c 351 MET cc_start: 0.9351 (mmm) cc_final: 0.8777 (mmm) REVERT: c 414 MET cc_start: 0.9375 (tmm) cc_final: 0.8913 (tmm) REVERT: c 417 LYS cc_start: 0.9236 (tppt) cc_final: 0.8877 (ttmm) outliers start: 29 outliers final: 23 residues processed: 124 average time/residue: 0.0799 time to fit residues: 14.5746 Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 347 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain a residue 403 ILE 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 203 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 347 ASP 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 212 CYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 403 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.052648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.041158 restraints weight = 57139.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.042524 restraints weight = 33421.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.043476 restraints weight = 24095.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.044106 restraints weight = 19568.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.044461 restraints weight = 17022.782| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5238 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 : 0.824 9.081 13848 Z= 0.395 Chirality : 0.044 0.245 1755 Planarity : 0.004 0.039 1587 Dihedral : 6.221 33.606 1170 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.11 % Favored : 86.33 % Rotamer: Outliers : 1.97 % Allowed : 13.56 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.24), residues: 1068 helix: -0.35 (0.27), residues: 399 sheet: 0.69 (0.65), residues: 57 loop : -2.64 (0.21), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 422 TYR 0.016 0.001 TYR A 150 PHE 0.010 0.001 PHE a 309 TRP 0.011 0.002 TRP b 283 HIS 0.009 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 9993) covalent geometry : angle 0.78054 / 0.39 (13536) SS BOND : bond 0.00660 / 0.40 ( 21) SS BOND : angle 1.95792 / 1.15 ( 42) hydrogen bonds : bond 0.04407 / 2.87 ( 333) hydrogen bonds : angle 5.36345 / 3.75 ( 891) link_ALPHA1-3 : bond 0.00554 / 0.34 ( 9) link_ALPHA1-3 : angle 2.95067 / 1.55 ( 27) link_ALPHA1-6 : bond 0.00347 / 0.20 ( 9) link_ALPHA1-6 : angle 1.54479 / 0.99 ( 27) link_BETA1-4 : bond 0.00510 / 0.29 ( 36) link_BETA1-4 : angle 1.69133 / 1.16 ( 108) link_BETA1-6 : bond 0.00405 / 0.20 ( 3) link_BETA1-6 : angle 1.41603 / 0.78 ( 9) link_NAG-ASN : bond 0.00379 / 0.23 ( 33) link_NAG-ASN : angle 1.94193 / 1.26 ( 99) *********************** 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 137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.414 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 82 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7936 (pmm) REVERT: A 134 MET cc_start: 0.8227 (ttp) cc_final: 0.7831 (tmm) REVERT: A 194 MET cc_start: 0.9141 (tpt) cc_final: 0.8913 (tpt) REVERT: a 311 ASP cc_start: 0.9172 (m-30) cc_final: 0.8730 (m-30) REVERT: a 320 LYS cc_start: 0.9528 (tptp) cc_final: 0.9182 (tptp) REVERT: B 82 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7669 (pmm) REVERT: B 153 MET cc_start: 0.6421 (mpp) cc_final: 0.6145 (mpp) REVERT: b 314 ARG cc_start: 0.9429 (ttm-80) cc_final: 0.9121 (ttm110) REVERT: b 399 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8537 (t80) REVERT: b 402 ASP cc_start: 0.8555 (m-30) cc_final: 0.7605 (m-30) REVERT: b 414 MET cc_start: 0.9372 (tmm) cc_final: 0.8956 (tmm) REVERT: C 194 MET cc_start: 0.9076 (tpt) cc_final: 0.8695 (tpp) REVERT: c 311 ASP cc_start: 0.9221 (m-30) cc_final: 0.8654 (m-30) REVERT: c 414 MET cc_start: 0.9394 (tmm) cc_final: 0.8823 (tmm) outliers start: 19 outliers final: 13 residues processed: 132 average time/residue: 0.1096 time to fit residues: 20.3400 Evaluate side-chains 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain a residue 402 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 399 PHE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 402 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 354 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.051615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.040323 restraints weight = 57721.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.041650 restraints weight = 33239.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.042590 restraints weight = 23685.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.043220 restraints weight = 19045.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.043594 restraints weight = 16457.511| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10104 Z= 0.211 Angle : 0.863 10.132 13848 Z= 0.412 Chirality : 0.044 0.195 1755 Planarity : 0.004 0.076 1587 Dihedral : 6.186 31.588 1170 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.17 % Favored : 87.36 % Rotamer: Outliers : 2.48 % Allowed : 14.70 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.24), residues: 1068 helix: -0.52 (0.26), residues: 405 sheet: 0.45 (0.56), residues: 75 loop : -2.69 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 248 TYR 0.018 0.002 TYR B 217 PHE 0.012 0.001 PHE a 309 TRP 0.035 0.002 TRP B 210 HIS 0.007 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 ( 9993) covalent geometry : angle 0.82270 / 0.40 (13536) SS BOND : bond 0.00702 / 0.42 ( 21) SS BOND : angle 1.81687 / 1.02 ( 42) hydrogen bonds : bond 0.04356 / 2.83 ( 333) hydrogen bonds : angle 5.45292 / 3.81 ( 891) link_ALPHA1-3 : bond 0.00475 / 0.28 ( 9) link_ALPHA1-3 : angle 2.73630 / 1.49 ( 27) link_ALPHA1-6 : bond 0.00225 / 0.12 ( 9) link_ALPHA1-6 : angle 1.72940 / 1.11 ( 27) link_BETA1-4 : bond 0.00454 / 0.26 ( 36) link_BETA1-4 : angle 1.72572 / 1.16 ( 108) link_BETA1-6 : bond 0.00204 / 0.10 ( 3) link_BETA1-6 : angle 1.47617 / 0.81 ( 9) link_NAG-ASN : bond 0.00258 / 0.15 ( 33) link_NAG-ASN : angle 1.98888 / 1.28 ( 99) *********************** 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 124 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7644 (pmm) REVERT: A 134 MET cc_start: 0.8351 (ttp) cc_final: 0.7951 (tmm) REVERT: a 311 ASP cc_start: 0.9191 (m-30) cc_final: 0.8736 (m-30) REVERT: a 320 LYS cc_start: 0.9549 (tptp) cc_final: 0.9197 (tptp) REVERT: a 414 MET cc_start: 0.9277 (tmm) cc_final: 0.8726 (tmm) REVERT: B 82 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7793 (pmm) REVERT: B 134 MET cc_start: 0.7811 (ttm) cc_final: 0.7215 (tmm) REVERT: B 153 MET cc_start: 0.6563 (mpp) cc_final: 0.6298 (mpp) REVERT: b 311 ASP cc_start: 0.9256 (m-30) cc_final: 0.8560 (m-30) REVERT: b 399 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8560 (t80) REVERT: b 402 ASP cc_start: 0.8544 (m-30) cc_final: 0.7573 (m-30) REVERT: b 414 MET cc_start: 0.9388 (tmm) cc_final: 0.8990 (tmm) REVERT: C 82 MET cc_start: 0.8823 (pmm) cc_final: 0.8483 (pmm) REVERT: C 194 MET cc_start: 0.9184 (tpt) cc_final: 0.8804 (tpp) REVERT: c 311 ASP cc_start: 0.9203 (m-30) cc_final: 0.8587 (m-30) REVERT: c 414 MET cc_start: 0.9387 (tmm) cc_final: 0.8830 (tmm) REVERT: c 417 LYS cc_start: 0.9236 (tppt) cc_final: 0.8890 (ttmm) outliers start: 24 outliers final: 13 residues processed: 119 average time/residue: 0.0849 time to fit residues: 15.0317 Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 402 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 212 CYS Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.052623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.041328 restraints weight = 56935.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.042700 restraints weight = 32704.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.043675 restraints weight = 23256.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.044308 restraints weight = 18667.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.044625 restraints weight = 16137.616| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10104 Z= 0.156 Angle : 0.824 11.399 13848 Z= 0.393 Chirality : 0.044 0.222 1755 Planarity : 0.004 0.045 1587 Dihedral : 5.982 30.607 1170 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.45 % Favored : 86.99 % Rotamer: Outliers : 1.76 % Allowed : 15.32 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.24), residues: 1068 helix: -0.48 (0.26), residues: 405 sheet: 0.00 (0.61), residues: 57 loop : -2.57 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 248 TYR 0.012 0.001 TYR A 150 PHE 0.009 0.001 PHE a 309 TRP 0.034 0.002 TRP C 210 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9993) covalent geometry : angle 0.78540 / 0.38 (13536) SS BOND : bond 0.00610 / 0.37 ( 21) SS BOND : angle 1.72829 / 0.95 ( 42) hydrogen bonds : bond 0.04123 / 2.72 ( 333) hydrogen bonds : angle 5.34391 / 3.73 ( 891) link_ALPHA1-3 : bond 0.00525 / 0.32 ( 9) link_ALPHA1-3 : angle 2.85924 / 1.52 ( 27) link_ALPHA1-6 : bond 0.00278 / 0.16 ( 9) link_ALPHA1-6 : angle 1.57354 / 1.01 ( 27) link_BETA1-4 : bond 0.00492 / 0.29 ( 36) link_BETA1-4 : angle 1.62460 / 1.11 ( 108) link_BETA1-6 : bond 0.00439 / 0.22 ( 3) link_BETA1-6 : angle 1.26609 / 0.70 ( 9) link_NAG-ASN : bond 0.00340 / 0.21 ( 33) link_NAG-ASN : angle 1.86297 / 1.21 ( 99) *********************** 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 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.511 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: 0.8133 (OUTLIER) cc_final: 0.7661 (pmm) REVERT: A 134 MET cc_start: 0.8328 (ttp) cc_final: 0.7932 (tmm) REVERT: a 311 ASP cc_start: 0.9153 (m-30) cc_final: 0.8716 (m-30) REVERT: a 312 MET cc_start: 0.9119 (tpp) cc_final: 0.8885 (tpp) REVERT: a 414 MET cc_start: 0.9289 (tmm) cc_final: 0.8797 (tmm) REVERT: B 82 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7678 (pmm) REVERT: B 134 MET cc_start: 0.7922 (ttm) cc_final: 0.7325 (tmm) REVERT: b 311 ASP cc_start: 0.9237 (m-30) cc_final: 0.8584 (m-30) REVERT: b 399 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8528 (t80) REVERT: b 402 ASP cc_start: 0.8505 (m-30) cc_final: 0.7445 (m-30) REVERT: b 414 MET cc_start: 0.9388 (tmm) cc_final: 0.8912 (tmm) REVERT: C 82 MET cc_start: 0.8789 (pmm) cc_final: 0.8357 (pmm) REVERT: C 153 MET cc_start: 0.6551 (mpp) cc_final: 0.6338 (mpp) REVERT: C 194 MET cc_start: 0.9065 (tpt) cc_final: 0.8656 (tpp) REVERT: c 311 ASP cc_start: 0.9240 (m-30) cc_final: 0.8612 (m-30) REVERT: c 414 MET cc_start: 0.9397 (tmm) cc_final: 0.8910 (tmm) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 0.0989 time to fit residues: 17.1959 Evaluate side-chains 114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain a residue 402 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 347 ASP 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 212 CYS Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 0.0570 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN B 69 GLN b 398 HIS C 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.052236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.041048 restraints weight = 57062.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.042390 restraints weight = 32509.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.043335 restraints weight = 23152.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.043893 restraints weight = 18620.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.044334 restraints weight = 16351.749| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10104 Z= 0.172 Angle : 0.854 11.820 13848 Z= 0.409 Chirality : 0.044 0.201 1755 Planarity : 0.004 0.055 1587 Dihedral : 5.926 29.785 1170 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.64 % Favored : 86.80 % Rotamer: Outliers : 1.55 % Allowed : 15.94 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.24), residues: 1068 helix: -0.38 (0.27), residues: 405 sheet: 0.24 (0.56), residues: 75 loop : -2.66 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG b 314 TYR 0.017 0.001 TYR A 150 PHE 0.010 0.001 PHE a 309 TRP 0.042 0.002 TRP C 210 HIS 0.006 0.001 HIS c 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 9993) covalent geometry : angle 0.81897 / 0.40 (13536) SS BOND : bond 0.00608 / 0.36 ( 21) SS BOND : angle 1.69629 / 0.92 ( 42) hydrogen bonds : bond 0.04030 / 2.64 ( 333) hydrogen bonds : angle 5.39109 / 3.75 ( 891) link_ALPHA1-3 : bond 0.00524 / 0.31 ( 9) link_ALPHA1-3 : angle 2.76799 / 1.49 ( 27) link_ALPHA1-6 : bond 0.00260 / 0.14 ( 9) link_ALPHA1-6 : angle 1.62532 / 1.04 ( 27) link_BETA1-4 : bond 0.00463 / 0.27 ( 36) link_BETA1-4 : angle 1.62547 / 1.10 ( 108) link_BETA1-6 : bond 0.00393 / 0.20 ( 3) link_BETA1-6 : angle 1.23450 / 0.68 ( 9) link_NAG-ASN : bond 0.00288 / 0.18 ( 33) link_NAG-ASN : angle 1.81785 / 1.18 ( 99) *********************** 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 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7769 (pmm) REVERT: A 134 MET cc_start: 0.8433 (ttp) cc_final: 0.8090 (tmm) REVERT: a 311 ASP cc_start: 0.9149 (m-30) cc_final: 0.8842 (t0) REVERT: a 312 MET cc_start: 0.9138 (tpp) cc_final: 0.8903 (tpp) REVERT: a 414 MET cc_start: 0.9296 (tmm) cc_final: 0.8814 (tmm) REVERT: B 82 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7686 (pmm) REVERT: B 134 MET cc_start: 0.7993 (ttm) cc_final: 0.7367 (tmm) REVERT: b 399 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8549 (t80) REVERT: b 402 ASP cc_start: 0.8487 (m-30) cc_final: 0.7388 (m-30) REVERT: b 414 MET cc_start: 0.9398 (tmm) cc_final: 0.8892 (tmm) REVERT: C 82 MET cc_start: 0.8807 (pmm) cc_final: 0.8407 (pmm) REVERT: C 194 MET cc_start: 0.9098 (tpt) cc_final: 0.8718 (tpp) REVERT: c 311 ASP cc_start: 0.9201 (m-30) cc_final: 0.8603 (m-30) REVERT: c 414 MET cc_start: 0.9395 (tmm) cc_final: 0.8911 (tmm) REVERT: c 417 LYS cc_start: 0.9207 (tppt) cc_final: 0.8874 (ttmm) outliers start: 15 outliers final: 12 residues processed: 113 average time/residue: 0.0932 time to fit residues: 15.5656 Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain a residue 402 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 399 PHE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 274 THR 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 60 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 78 optimal weight: 0.2980 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.052988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.041853 restraints weight = 56132.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.043218 restraints weight = 31744.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.044161 restraints weight = 22597.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.044806 restraints weight = 18155.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.045166 restraints weight = 15652.764| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10104 Z= 0.154 Angle : 0.844 12.578 13848 Z= 0.402 Chirality : 0.044 0.206 1755 Planarity : 0.004 0.052 1587 Dihedral : 5.810 28.887 1170 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.36 % Favored : 87.17 % Rotamer: Outliers : 1.86 % Allowed : 15.94 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.24), residues: 1068 helix: -0.05 (0.27), residues: 387 sheet: -0.07 (0.63), residues: 57 loop : -2.60 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG b 314 TYR 0.018 0.001 TYR A 150 PHE 0.008 0.001 PHE a 309 TRP 0.047 0.002 TRP C 210 HIS 0.004 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9993) covalent geometry : angle 0.81084 / 0.40 (13536) SS BOND : bond 0.00552 / 0.34 ( 21) SS BOND : angle 1.59121 / 0.84 ( 42) hydrogen bonds : bond 0.03883 / 2.58 ( 333) hydrogen bonds : angle 5.29127 / 3.68 ( 891) link_ALPHA1-3 : bond 0.00553 / 0.33 ( 9) link_ALPHA1-3 : angle 2.80802 / 1.50 ( 27) link_ALPHA1-6 : bond 0.00321 / 0.19 ( 9) link_ALPHA1-6 : angle 1.56040 / 1.00 ( 27) link_BETA1-4 : bond 0.00474 / 0.27 ( 36) link_BETA1-4 : angle 1.57013 / 1.07 ( 108) link_BETA1-6 : bond 0.00528 / 0.26 ( 3) link_BETA1-6 : angle 1.22414 / 0.66 ( 9) link_NAG-ASN : bond 0.00366 / 0.22 ( 33) link_NAG-ASN : angle 1.74505 / 1.14 ( 99) ********************** 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 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.231 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: 0.8231 (OUTLIER) cc_final: 0.7659 (pmm) REVERT: A 134 MET cc_start: 0.8397 (ttp) cc_final: 0.8095 (tmm) REVERT: A 210 TRP cc_start: 0.5716 (t-100) cc_final: 0.5437 (t-100) REVERT: a 311 ASP cc_start: 0.9087 (m-30) cc_final: 0.8735 (t0) REVERT: a 312 MET cc_start: 0.9150 (tpp) cc_final: 0.8921 (tpp) REVERT: a 414 MET cc_start: 0.9315 (tmm) cc_final: 0.8839 (tmm) REVERT: B 82 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7582 (pmm) REVERT: B 134 MET cc_start: 0.8003 (ttm) cc_final: 0.7326 (tmm) REVERT: b 311 ASP cc_start: 0.9230 (m-30) cc_final: 0.8570 (m-30) REVERT: b 332 MET cc_start: 0.8781 (tpp) cc_final: 0.8074 (tpp) REVERT: b 399 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8374 (t80) REVERT: b 402 ASP cc_start: 0.8448 (m-30) cc_final: 0.7293 (m-30) REVERT: b 414 MET cc_start: 0.9395 (tmm) cc_final: 0.8928 (tmm) REVERT: C 80 MET cc_start: 0.9482 (tpp) cc_final: 0.8931 (tpp) REVERT: C 82 MET cc_start: 0.8756 (pmm) cc_final: 0.8379 (pmm) REVERT: C 153 MET cc_start: 0.6622 (mpp) cc_final: 0.6339 (mpp) REVERT: C 194 MET cc_start: 0.9031 (tpt) cc_final: 0.8635 (tpp) REVERT: c 311 ASP cc_start: 0.9171 (m-30) cc_final: 0.8622 (m-30) REVERT: c 332 MET cc_start: 0.8243 (mtp) cc_final: 0.7946 (mtp) REVERT: c 414 MET cc_start: 0.9395 (tmm) cc_final: 0.8925 (tmm) REVERT: c 417 LYS cc_start: 0.9219 (tppt) cc_final: 0.8952 (ttmm) outliers start: 18 outliers final: 10 residues processed: 120 average time/residue: 0.0710 time to fit residues: 12.6112 Evaluate side-chains 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain a residue 402 ASP Chi-restraints excluded: chain B residue 82 MET 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 192 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 274 THR 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 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 81 optimal weight: 0.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.052952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.041842 restraints weight = 56343.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.043250 restraints weight = 31953.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.044212 restraints weight = 22524.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.044865 restraints weight = 17971.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.045181 restraints weight = 15459.847| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10104 Z= 0.150 Angle : 0.844 10.751 13848 Z= 0.406 Chirality : 0.043 0.257 1755 Planarity : 0.004 0.049 1587 Dihedral : 5.589 28.105 1170 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.27 % Favored : 87.27 % Rotamer: Outliers : 1.24 % Allowed : 16.56 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.25), residues: 1068 helix: 0.06 (0.28), residues: 387 sheet: 0.37 (0.57), residues: 75 loop : -2.66 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 178 TYR 0.016 0.001 TYR A 150 PHE 0.020 0.001 PHE B 117 TRP 0.046 0.002 TRP C 210 HIS 0.005 0.001 HIS c 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9993) covalent geometry : angle 0.81243 / 0.40 (13536) SS BOND : bond 0.00515 / 0.32 ( 21) SS BOND : angle 1.65643 / 0.87 ( 42) hydrogen bonds : bond 0.03939 / 2.59 ( 333) hydrogen bonds : angle 5.35618 / 3.74 ( 891) link_ALPHA1-3 : bond 0.00579 / 0.35 ( 9) link_ALPHA1-3 : angle 2.82107 / 1.51 ( 27) link_ALPHA1-6 : bond 0.00322 / 0.19 ( 9) link_ALPHA1-6 : angle 1.53666 / 0.99 ( 27) link_BETA1-4 : bond 0.00484 / 0.28 ( 36) link_BETA1-4 : angle 1.58096 / 1.08 ( 108) link_BETA1-6 : bond 0.00567 / 0.28 ( 3) link_BETA1-6 : angle 1.20467 / 0.65 ( 9) link_NAG-ASN : bond 0.00333 / 0.18 ( 33) link_NAG-ASN : angle 1.58849 / 1.06 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1365.74 seconds wall clock time: 24 minutes 50.93 seconds (1490.93 seconds total)