Starting phenix.real_space_refine on Fri Jul 3 00:39:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eji_28183/07_2026/8eji_28183.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eji_28183/07_2026/8eji_28183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eji_28183/07_2026/8eji_28183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eji_28183/07_2026/8eji_28183.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8eji_28183/07_2026/8eji_28183.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eji_28183/07_2026/8eji_28183.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eji_28183/07_2026/8eji_28183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eji_28183/07_2026/8eji_28183.map" } resolution = 3.81 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= 0.003 sd= 0.032 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 97 5.16 5 C 6886 2.51 5 N 1742 2.21 5 O 2298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11023 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "a" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1286 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "B" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1504 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain breaks: 1 Chain: "b" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1223 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 3, 'TRANS': 146} Chain breaks: 1 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1504 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain breaks: 1 Chain: "c" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1232 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 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: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "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: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 2.14, per 1000 atoms: 0.19 Number of scatterers: 11023 At special positions: 0 Unit cell: (125.4, 96.14, 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 97 16.00 O 2298 8.00 N 1742 7.00 C 6886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.04 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.01 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.08 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 H 23 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.02 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.08 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 ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " MAN E 4 " - " MAN E 5 " " BMA G 3 " - " MAN G 5 " " BMA M 3 " - " MAN M 5 " " BMA R 3 " - " MAN R 6 " " BMA W 3 " - " MAN W 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG B 301 " - " ASN B 89 " " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 109 " " NAG B 304 " - " ASN B 119 " " NAG C 301 " - " ASN C 89 " " NAG C 302 " - " ASN C 99 " " NAG C 303 " - " ASN C 109 " " NAG C 304 " - " ASN C 119 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 99 " " NAG G 1 " - " ASN A 109 " " NAG I 1 " - " ASN A 119 " " NAG J 1 " - " ASN A 167 " " NAG K 1 " - " ASN A 224 " " NAG M 1 " - " ASN a 365 " " NAG N 1 " - " ASN a 373 " " NAG O 1 " - " ASN B 79 " " 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 167 " " NAG V 1 " - " ASN C 224 " " NAG W 1 " - " ASN c 365 " " NAG X 1 " - " ASN c 373 " " 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 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 357.9 milliseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2362 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 37.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 209 through 213 removed outlier: 3.946A pdb=" N ILE A 213 " --> pdb=" O TRP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.603A pdb=" N LEU A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 304 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 329 through 333 removed outlier: 3.541A pdb=" N SER a 333 " --> pdb=" O ALA a 330 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 339 Processing helix chain 'a' and resid 340 through 345 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.587A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 418 removed outlier: 5.603A pdb=" N ASP a 401 " --> pdb=" O THR a 397 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASP a 402 " --> pdb=" O HIS a 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.544A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 195 through 203 removed outlier: 4.384A pdb=" N TYR B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.819A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 294 through 302 removed outlier: 3.559A pdb=" N ASN b 302 " --> pdb=" O VAL b 298 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 333 through 345 removed outlier: 3.894A pdb=" N LYS b 339 " --> pdb=" O GLN b 335 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.603A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 417 Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 96 through 100 Processing helix chain 'L' and resid 95 through 99 removed outlier: 4.017A pdb=" N PHE L 99 " --> pdb=" O PRO L 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.543A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 195 through 203 removed outlier: 4.385A pdb=" N TYR C 200 " --> pdb=" O TRP C 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.818A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 294 through 302 removed outlier: 3.559A pdb=" N ASN c 302 " --> pdb=" O VAL c 298 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 333 through 345 removed outlier: 3.895A pdb=" N LYS c 339 " --> pdb=" O GLN c 335 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.604A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.628A pdb=" N GLY A 102 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 279 through 281 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 61 through 62 Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 72 removed outlier: 9.249A pdb=" N TYR b 366 " --> pdb=" O VAL b 388 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N VAL b 388 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS b 368 " --> pdb=" O TRP b 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AA8, first strand: chain 'b' and resid 278 through 280 removed outlier: 3.635A pdb=" N LYS b 291 " --> pdb=" O LEU b 280 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.923A pdb=" N MET H 39 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.563A pdb=" N LEU L 11 " --> pdb=" O ASP L 125 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU L 39 " --> pdb=" O ASN L 55 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.563A pdb=" N LEU L 11 " --> pdb=" O ASP L 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AB7, first strand: chain 'C' and resid 71 through 72 removed outlier: 9.249A pdb=" N TYR c 366 " --> pdb=" O VAL c 388 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N VAL c 388 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS c 368 " --> pdb=" O TRP c 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AB9, first strand: chain 'c' and resid 278 through 280 removed outlier: 3.635A pdb=" N LYS c 291 " --> pdb=" O LEU c 280 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1185 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: 1.62 Time building geometry restraints manager: 1.29 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: 2105 1.32 - 1.45: 3702 1.45 - 1.59: 5255 1.59 - 1.72: 36 1.72 - 1.86: 146 Bond restraints: 11244 Sorted by residual: bond pdb=" CB HIS A 170 " pdb=" CG HIS A 170 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.16e+01 bond pdb=" CB HIS A 93 " pdb=" CG HIS A 93 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.71e+01 bond pdb=" CB HIS a 354 " pdb=" CG HIS a 354 " ideal model delta sigma weight residual 1.497 1.414 0.083 1.40e-02 5.10e+03 3.55e+01 bond pdb=" CB LEU a 372 " pdb=" CG LEU a 372 " ideal model delta sigma weight residual 1.530 1.422 0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" CB HIS H 40 " pdb=" CG HIS H 40 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.76e+01 ... (remaining 11239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 13396 2.73 - 5.47: 1597 5.47 - 8.20: 200 8.20 - 10.93: 27 10.93 - 13.66: 6 Bond angle restraints: 15226 Sorted by residual: angle pdb=" N LEU a 382 " pdb=" CA LEU a 382 " pdb=" C LEU a 382 " ideal model delta sigma weight residual 109.83 99.24 10.59 1.27e+00 6.20e-01 6.96e+01 angle pdb=" C SER a 267 " pdb=" CA SER a 267 " pdb=" CB SER a 267 " ideal model delta sigma weight residual 117.23 107.05 10.18 1.36e+00 5.41e-01 5.61e+01 angle pdb=" C TRP c 370 " pdb=" CA TRP c 370 " pdb=" CB TRP c 370 " ideal model delta sigma weight residual 110.85 98.41 12.44 1.70e+00 3.46e-01 5.36e+01 angle pdb=" C TRP b 370 " pdb=" CA TRP b 370 " pdb=" CB TRP b 370 " ideal model delta sigma weight residual 110.85 98.45 12.40 1.70e+00 3.46e-01 5.32e+01 angle pdb=" N LEU c 382 " pdb=" CA LEU c 382 " pdb=" C LEU c 382 " ideal model delta sigma weight residual 109.50 99.00 10.50 1.47e+00 4.63e-01 5.10e+01 ... (remaining 15221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5844 17.81 - 35.62: 179 35.62 - 53.43: 63 53.43 - 71.24: 15 71.24 - 89.04: 10 Dihedral angle restraints: 6111 sinusoidal: 2443 harmonic: 3668 Sorted by residual: dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 105 " pdb=" CB CYS H 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.90 -73.90 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual -86.00 -158.57 72.57 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 231 " pdb=" CB CYS B 231 " ideal model delta sinusoidal sigma weight residual -86.00 -158.53 72.53 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 6108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1292 0.119 - 0.239: 409 0.239 - 0.358: 146 0.358 - 0.478: 62 0.478 - 0.597: 9 Chirality restraints: 1918 Sorted by residual: chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-02 2.50e+03 6.36e+02 chirality pdb=" C1 BMA W 3 " pdb=" O4 NAG W 2 " pdb=" C2 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.47e+02 chirality pdb=" C1 MAN W 5 " pdb=" O2 MAN W 4 " pdb=" C2 MAN W 5 " pdb=" O5 MAN W 5 " both_signs ideal model delta sigma weight residual False 2.40 2.75 -0.35 2.00e-02 2.50e+03 3.00e+02 ... (remaining 1915 not shown) Planarity restraints: 1836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG S 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 2 " 0.355 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG X 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG X 2 " 0.131 2.00e-02 2.50e+03 pdb=" N2 NAG X 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG X 2 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.349 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG R 1 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.089 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " -0.179 2.00e-02 2.50e+03 ... (remaining 1833 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3323 2.83 - 3.35: 10668 3.35 - 3.86: 18681 3.86 - 4.38: 22634 4.38 - 4.90: 35563 Nonbonded interactions: 90869 Sorted by model distance: nonbonded pdb=" O4 MAN J 4 " pdb=" O6 MAN J 4 " model vdw 2.309 3.040 nonbonded pdb=" NZ LYS a 339 " pdb=" OD2 ASP B 251 " model vdw 2.409 3.120 nonbonded pdb=" OD2 ASP H 82 " pdb=" NZ LYS H 85 " model vdw 2.410 3.120 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 2.419 3.040 nonbonded pdb=" N ASP c 306 " pdb=" OD1 ASP c 306 " model vdw 2.419 3.120 ... (remaining 90864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 59 through 171 or resid 179 through 255)) selection = (chain 'B' and resid 59 through 255) selection = (chain 'C' and resid 59 through 255) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'R' selection = chain 'W' } ncs_group { reference = (chain 'a' and (resid 260 through 268 or resid 277 through 417 or resid 701 thro \ ugh 702)) selection = chain 'b' selection = (chain 'c' and (resid 260 through 417 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.140 Find NCS groups from input model: 0.210 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: 13.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.023 0.134 11345 Z= 1.213 Angle : 1.907 13.663 15506 Z= 1.172 Chirality : 0.148 0.597 1918 Planarity : 0.018 0.306 1803 Dihedral : 10.705 89.045 3680 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.23), residues: 1231 helix: -0.12 (0.25), residues: 358 sheet: 0.71 (0.33), residues: 232 loop : 0.27 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 248 TYR 0.056 0.009 TYR a 363 PHE 0.034 0.006 PHE L 118 TRP 0.034 0.009 TRP A 196 HIS 0.015 0.003 HIS c 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02204 / 1.19 (11244) covalent geometry : angle 1.84806 / 1.17 (15226) SS BOND : bond 0.01612 / 1.11 ( 23) SS BOND : angle 2.62679 / 1.76 ( 46) hydrogen bonds : bond 0.17826 / 12.08 ( 447) hydrogen bonds : angle 7.33024 / 5.15 ( 1185) link_ALPHA1-2 : bond 0.00488 / 0.24 ( 2) link_ALPHA1-2 : angle 5.91152 / 3.12 ( 6) link_ALPHA1-3 : bond 0.06881 / 3.99 ( 7) link_ALPHA1-3 : angle 4.50911 / 2.72 ( 21) link_ALPHA1-6 : bond 0.05289 / 2.58 ( 5) link_ALPHA1-6 : angle 2.76301 / 1.46 ( 15) link_BETA1-4 : bond 0.06286 / 4.17 ( 31) link_BETA1-4 : angle 4.77463 / 3.03 ( 93) link_NAG-ASN : bond 0.06888 / 4.34 ( 33) link_NAG-ASN : angle 3.47607 / 2.16 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.245 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: 0.9141 (ptp) cc_final: 0.8918 (ptp) REVERT: A 134 MET cc_start: 0.9087 (tpp) cc_final: 0.8265 (tpp) REVERT: a 284 MET cc_start: 0.9002 (mtp) cc_final: 0.8580 (mtt) REVERT: a 347 ASP cc_start: 0.8227 (p0) cc_final: 0.7864 (p0) REVERT: a 405 GLN cc_start: 0.8905 (tp40) cc_final: 0.8533 (tp-100) REVERT: a 408 ASP cc_start: 0.8508 (m-30) cc_final: 0.8102 (t70) REVERT: b 289 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7129 (pm20) REVERT: b 312 MET cc_start: 0.8916 (mmm) cc_final: 0.8693 (mmm) REVERT: H 39 MET cc_start: 0.8371 (mmm) cc_final: 0.8029 (mmt) REVERT: H 126 VAL cc_start: 0.9228 (t) cc_final: 0.9008 (p) REVERT: L 98 ASP cc_start: 0.8550 (m-30) cc_final: 0.8193 (m-30) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.0932 time to fit residues: 43.1416 Evaluate side-chains 145 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 170 HIS A 179 HIS A 247 GLN ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** b 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.079539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.066636 restraints weight = 37026.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.068808 restraints weight = 22602.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.070360 restraints weight = 16323.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.071429 restraints weight = 12860.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072212 restraints weight = 10783.018| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11345 Z= 0.202 Angle : 0.997 16.069 15506 Z= 0.463 Chirality : 0.050 0.303 1918 Planarity : 0.004 0.034 1803 Dihedral : 5.714 18.670 1343 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.82 % Favored : 96.10 % Rotamer: Outliers : 2.40 % Allowed : 9.78 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.23), residues: 1231 helix: 0.60 (0.26), residues: 370 sheet: 1.04 (0.36), residues: 198 loop : -0.49 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 81 TYR 0.017 0.002 TYR A 66 PHE 0.022 0.002 PHE C 117 TRP 0.032 0.003 TRP c 370 HIS 0.007 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (11244) covalent geometry : angle 0.88131 / 0.44 (15226) SS BOND : bond 0.00368 / 0.27 ( 23) SS BOND : angle 1.62825 / 1.08 ( 46) hydrogen bonds : bond 0.05608 / 3.71 ( 447) hydrogen bonds : angle 5.47229 / 3.88 ( 1185) link_ALPHA1-2 : bond 0.00132 / 0.06 ( 2) link_ALPHA1-2 : angle 2.15347 / 1.10 ( 6) link_ALPHA1-3 : bond 0.00712 / 0.40 ( 7) link_ALPHA1-3 : angle 2.45562 / 1.47 ( 21) link_ALPHA1-6 : bond 0.00623 / 0.30 ( 5) link_ALPHA1-6 : angle 1.39207 / 0.85 ( 15) link_BETA1-4 : bond 0.00752 / 0.46 ( 31) link_BETA1-4 : angle 3.66539 / 2.38 ( 93) link_NAG-ASN : bond 0.00948 / 0.56 ( 33) link_NAG-ASN : angle 4.54690 / 2.70 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9022 (tpp) cc_final: 0.7730 (tpp) REVERT: A 150 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: A 194 MET cc_start: 0.8942 (tpp) cc_final: 0.8714 (tpp) REVERT: A 210 TRP cc_start: 0.7462 (t60) cc_final: 0.7258 (t60) REVERT: a 311 ASP cc_start: 0.8854 (m-30) cc_final: 0.8600 (t70) REVERT: a 332 MET cc_start: 0.8434 (tmm) cc_final: 0.7610 (tmm) REVERT: a 347 ASP cc_start: 0.8027 (p0) cc_final: 0.7332 (p0) REVERT: B 189 GLN cc_start: 0.8704 (mt0) cc_final: 0.8420 (tt0) REVERT: b 347 ASP cc_start: 0.7404 (p0) cc_final: 0.6979 (p0) REVERT: L 106 GLN cc_start: 0.7715 (pp30) cc_final: 0.7422 (pp30) REVERT: c 312 MET cc_start: 0.8917 (mmm) cc_final: 0.8115 (mmm) outliers start: 27 outliers final: 13 residues processed: 207 average time/residue: 0.0838 time to fit residues: 25.4280 Evaluate side-chains 155 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 150 TYR Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 345 ILE Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN A 179 HIS ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 185 ASN L 43 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.074444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.059559 restraints weight = 37941.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.062093 restraints weight = 20002.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.063821 restraints weight = 13512.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.065011 restraints weight = 10418.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065839 restraints weight = 8663.539| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11345 Z= 0.272 Angle : 0.956 13.950 15506 Z= 0.440 Chirality : 0.048 0.304 1918 Planarity : 0.004 0.043 1803 Dihedral : 5.594 21.436 1343 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.20 % Allowed : 12.36 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1231 helix: 0.77 (0.27), residues: 375 sheet: 0.86 (0.34), residues: 221 loop : -0.96 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG a 282 TYR 0.023 0.002 TYR A 62 PHE 0.016 0.002 PHE C 117 TRP 0.025 0.003 TRP b 283 HIS 0.011 0.002 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 (11244) covalent geometry : angle 0.86538 / 0.42 (15226) SS BOND : bond 0.00543 / 0.36 ( 23) SS BOND : angle 1.59580 / 1.06 ( 46) hydrogen bonds : bond 0.05061 / 3.34 ( 447) hydrogen bonds : angle 5.20412 / 3.67 ( 1185) link_ALPHA1-2 : bond 0.00489 / 0.24 ( 2) link_ALPHA1-2 : angle 2.21219 / 1.11 ( 6) link_ALPHA1-3 : bond 0.00546 / 0.26 ( 7) link_ALPHA1-3 : angle 2.22547 / 1.34 ( 21) link_ALPHA1-6 : bond 0.00605 / 0.28 ( 5) link_ALPHA1-6 : angle 1.58744 / 0.93 ( 15) link_BETA1-4 : bond 0.00620 / 0.41 ( 31) link_BETA1-4 : angle 2.91648 / 1.83 ( 93) link_NAG-ASN : bond 0.00590 / 0.39 ( 33) link_NAG-ASN : angle 4.14555 / 2.44 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9241 (tpp) cc_final: 0.7675 (tpp) REVERT: A 194 MET cc_start: 0.9246 (tpp) cc_final: 0.9034 (tpp) REVERT: a 307 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8121 (mt-10) REVERT: a 311 ASP cc_start: 0.9260 (m-30) cc_final: 0.8950 (t70) REVERT: a 332 MET cc_start: 0.8868 (tmm) cc_final: 0.7706 (tmm) REVERT: a 347 ASP cc_start: 0.8389 (p0) cc_final: 0.7772 (p0) REVERT: a 353 ASN cc_start: 0.9118 (m-40) cc_final: 0.8903 (m-40) REVERT: a 382 LEU cc_start: 0.9175 (tt) cc_final: 0.8866 (tt) REVERT: B 134 MET cc_start: 0.8644 (tpp) cc_final: 0.8237 (tpp) REVERT: B 192 MET cc_start: 0.8709 (tpp) cc_final: 0.8334 (tpp) REVERT: H 39 MET cc_start: 0.8569 (mmm) cc_final: 0.8283 (mmm) REVERT: L 17 ASP cc_start: 0.7767 (m-30) cc_final: 0.7512 (p0) REVERT: L 87 PHE cc_start: 0.8277 (m-80) cc_final: 0.7804 (m-10) REVERT: L 89 LEU cc_start: 0.8544 (tp) cc_final: 0.8306 (tp) REVERT: L 97 ASP cc_start: 0.8909 (t0) cc_final: 0.8606 (t0) REVERT: L 106 GLN cc_start: 0.8003 (pp30) cc_final: 0.7646 (pp30) REVERT: C 96 MET cc_start: 0.7297 (mtm) cc_final: 0.6887 (mmm) REVERT: C 251 ASP cc_start: 0.8027 (m-30) cc_final: 0.7820 (m-30) REVERT: c 348 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8547 (mm-40) REVERT: c 351 MET cc_start: 0.8801 (tpp) cc_final: 0.8474 (mmm) REVERT: c 361 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8380 (tp) REVERT: c 368 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7349 (mtpp) REVERT: c 370 TRP cc_start: 0.7872 (m-10) cc_final: 0.7519 (m-10) REVERT: c 414 MET cc_start: 0.9389 (ppp) cc_final: 0.9141 (ppp) outliers start: 36 outliers final: 24 residues processed: 171 average time/residue: 0.0824 time to fit residues: 20.5850 Evaluate side-chains 160 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain H residue 81 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 368 LYS Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 40 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 93 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 305 HIS a 405 GLN C 93 HIS C 146 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062155 restraints weight = 37985.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.064720 restraints weight = 20467.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066490 restraints weight = 13950.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.067723 restraints weight = 10777.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.068583 restraints weight = 8935.197| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11345 Z= 0.137 Angle : 0.798 12.977 15506 Z= 0.368 Chirality : 0.044 0.269 1918 Planarity : 0.003 0.042 1803 Dihedral : 5.276 20.574 1343 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.58 % Allowed : 13.07 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.23), residues: 1231 helix: 0.87 (0.27), residues: 376 sheet: 0.93 (0.34), residues: 221 loop : -0.93 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 314 TYR 0.020 0.002 TYR A 62 PHE 0.013 0.002 PHE C 117 TRP 0.021 0.002 TRP C 227 HIS 0.011 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (11244) covalent geometry : angle 0.71996 / 0.35 (15226) SS BOND : bond 0.00297 / 0.20 ( 23) SS BOND : angle 1.02648 / 0.68 ( 46) hydrogen bonds : bond 0.04038 / 2.66 ( 447) hydrogen bonds : angle 4.95406 / 3.53 ( 1185) link_ALPHA1-2 : bond 0.00203 / 0.10 ( 2) link_ALPHA1-2 : angle 1.92602 / 1.01 ( 6) link_ALPHA1-3 : bond 0.00526 / 0.26 ( 7) link_ALPHA1-3 : angle 1.98216 / 1.20 ( 21) link_ALPHA1-6 : bond 0.00566 / 0.28 ( 5) link_ALPHA1-6 : angle 1.48388 / 0.88 ( 15) link_BETA1-4 : bond 0.00581 / 0.38 ( 31) link_BETA1-4 : angle 2.37474 / 1.49 ( 93) link_NAG-ASN : bond 0.00530 / 0.33 ( 33) link_NAG-ASN : angle 3.58813 / 2.11 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7481 (mtp) cc_final: 0.7031 (mtt) REVERT: A 194 MET cc_start: 0.9116 (tpp) cc_final: 0.8900 (tpp) REVERT: a 303 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7705 (tm-30) REVERT: a 311 ASP cc_start: 0.9195 (m-30) cc_final: 0.8836 (t70) REVERT: a 347 ASP cc_start: 0.8403 (p0) cc_final: 0.7795 (p0) REVERT: B 94 TYR cc_start: 0.8023 (m-80) cc_final: 0.7656 (m-80) REVERT: B 134 MET cc_start: 0.8582 (tpp) cc_final: 0.7728 (tpp) REVERT: B 192 MET cc_start: 0.8467 (tpp) cc_final: 0.7846 (tpp) REVERT: b 347 ASP cc_start: 0.7954 (p0) cc_final: 0.7636 (p0) REVERT: L 87 PHE cc_start: 0.8153 (m-80) cc_final: 0.7464 (m-10) REVERT: L 89 LEU cc_start: 0.8661 (tp) cc_final: 0.8368 (tp) REVERT: L 97 ASP cc_start: 0.8878 (t0) cc_final: 0.8441 (t0) REVERT: L 106 GLN cc_start: 0.7771 (pp30) cc_final: 0.7341 (pp30) REVERT: C 100 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7180 (mm-30) REVERT: C 228 GLU cc_start: 0.8144 (pp20) cc_final: 0.7604 (tp30) REVERT: c 361 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8576 (tt) REVERT: c 370 TRP cc_start: 0.7349 (m-10) cc_final: 0.7094 (m-10) outliers start: 29 outliers final: 13 residues processed: 181 average time/residue: 0.0860 time to fit residues: 22.6901 Evaluate side-chains 155 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.0670 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 335 GLN C 146 ASN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.058414 restraints weight = 37708.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060827 restraints weight = 20231.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.062454 restraints weight = 13778.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.063608 restraints weight = 10690.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.064413 restraints weight = 8904.487| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11345 Z= 0.259 Angle : 0.883 13.483 15506 Z= 0.408 Chirality : 0.046 0.312 1918 Planarity : 0.004 0.048 1803 Dihedral : 5.300 21.914 1343 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.67 % Allowed : 14.22 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.23), residues: 1231 helix: 1.06 (0.28), residues: 371 sheet: 0.69 (0.34), residues: 221 loop : -1.12 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 81 TYR 0.022 0.002 TYR L 107 PHE 0.016 0.002 PHE C 147 TRP 0.022 0.002 TRP C 227 HIS 0.011 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.26 (11244) covalent geometry : angle 0.80955 / 0.39 (15226) SS BOND : bond 0.00447 / 0.31 ( 23) SS BOND : angle 1.13289 / 0.78 ( 46) hydrogen bonds : bond 0.04381 / 2.92 ( 447) hydrogen bonds : angle 4.98330 / 3.54 ( 1185) link_ALPHA1-2 : bond 0.00376 / 0.18 ( 2) link_ALPHA1-2 : angle 2.24535 / 1.16 ( 6) link_ALPHA1-3 : bond 0.00486 / 0.21 ( 7) link_ALPHA1-3 : angle 1.95035 / 1.18 ( 21) link_ALPHA1-6 : bond 0.00558 / 0.26 ( 5) link_ALPHA1-6 : angle 1.64071 / 0.95 ( 15) link_BETA1-4 : bond 0.00497 / 0.33 ( 31) link_BETA1-4 : angle 2.43485 / 1.51 ( 93) link_NAG-ASN : bond 0.00537 / 0.35 ( 33) link_NAG-ASN : angle 3.68937 / 2.17 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8894 (mpp) REVERT: A 96 MET cc_start: 0.7595 (mtp) cc_final: 0.7218 (mtt) REVERT: A 134 MET cc_start: 0.9266 (tpp) cc_final: 0.7486 (tpp) REVERT: A 162 ILE cc_start: 0.9491 (mt) cc_final: 0.9282 (mm) REVERT: a 262 PHE cc_start: 0.6925 (p90) cc_final: 0.6628 (p90) REVERT: a 303 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7826 (tm-30) REVERT: a 307 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: a 311 ASP cc_start: 0.9296 (m-30) cc_final: 0.9000 (t0) REVERT: a 332 MET cc_start: 0.9020 (tmm) cc_final: 0.8556 (tmm) REVERT: a 347 ASP cc_start: 0.8502 (p0) cc_final: 0.8214 (p0) REVERT: B 67 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7284 (tm-30) REVERT: B 96 MET cc_start: 0.7829 (mtm) cc_final: 0.7615 (mtm) REVERT: B 134 MET cc_start: 0.8633 (tpp) cc_final: 0.7515 (tpp) REVERT: B 192 MET cc_start: 0.8495 (tpp) cc_final: 0.7904 (tpp) REVERT: b 284 MET cc_start: 0.7671 (ptt) cc_final: 0.7445 (mtm) REVERT: b 312 MET cc_start: 0.8841 (mmm) cc_final: 0.8596 (mmp) REVERT: b 347 ASP cc_start: 0.7911 (p0) cc_final: 0.7709 (p0) REVERT: L 87 PHE cc_start: 0.8164 (m-80) cc_final: 0.7829 (m-10) REVERT: L 89 LEU cc_start: 0.8668 (tp) cc_final: 0.8342 (tp) REVERT: L 97 ASP cc_start: 0.9009 (t0) cc_final: 0.8577 (t0) REVERT: L 106 GLN cc_start: 0.8274 (pp30) cc_final: 0.7894 (pp30) REVERT: L 120 GLN cc_start: 0.8381 (pm20) cc_final: 0.8123 (pm20) REVERT: C 228 GLU cc_start: 0.8071 (pp20) cc_final: 0.7589 (tp30) REVERT: c 312 MET cc_start: 0.8902 (mmm) cc_final: 0.8624 (tpp) REVERT: c 361 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8512 (tp) REVERT: c 370 TRP cc_start: 0.7802 (m-10) cc_final: 0.7346 (m-10) outliers start: 30 outliers final: 17 residues processed: 159 average time/residue: 0.0809 time to fit residues: 18.9625 Evaluate side-chains 146 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 80 optimal weight: 0.0670 chunk 69 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.060996 restraints weight = 37788.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.063527 restraints weight = 20421.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.065260 restraints weight = 13990.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066465 restraints weight = 10863.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.067307 restraints weight = 9061.949| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11345 Z= 0.131 Angle : 0.757 12.839 15506 Z= 0.350 Chirality : 0.044 0.353 1918 Planarity : 0.003 0.047 1803 Dihedral : 5.047 20.616 1343 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.69 % Allowed : 15.29 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.24), residues: 1231 helix: 1.11 (0.27), residues: 374 sheet: 0.75 (0.34), residues: 227 loop : -0.96 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 81 TYR 0.018 0.001 TYR B 219 PHE 0.023 0.002 PHE c 262 TRP 0.011 0.001 TRP b 283 HIS 0.013 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (11244) covalent geometry : angle 0.69130 / 0.34 (15226) SS BOND : bond 0.00268 / 0.19 ( 23) SS BOND : angle 0.80865 / 0.53 ( 46) hydrogen bonds : bond 0.03703 / 2.47 ( 447) hydrogen bonds : angle 4.79789 / 3.43 ( 1185) link_ALPHA1-2 : bond 0.00195 / 0.10 ( 2) link_ALPHA1-2 : angle 1.92670 / 1.01 ( 6) link_ALPHA1-3 : bond 0.00496 / 0.23 ( 7) link_ALPHA1-3 : angle 1.86437 / 1.13 ( 21) link_ALPHA1-6 : bond 0.00557 / 0.28 ( 5) link_ALPHA1-6 : angle 1.48278 / 0.89 ( 15) link_BETA1-4 : bond 0.00537 / 0.35 ( 31) link_BETA1-4 : angle 2.08298 / 1.30 ( 93) link_NAG-ASN : bond 0.00495 / 0.30 ( 33) link_NAG-ASN : angle 3.26593 / 1.90 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9092 (ptp) cc_final: 0.8781 (mpp) REVERT: A 96 MET cc_start: 0.7504 (mtp) cc_final: 0.7174 (mtt) REVERT: A 134 MET cc_start: 0.9234 (tpp) cc_final: 0.7352 (tpp) REVERT: A 230 HIS cc_start: 0.7703 (m-70) cc_final: 0.7400 (m170) REVERT: a 303 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7659 (tm-30) REVERT: a 307 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: a 311 ASP cc_start: 0.9259 (m-30) cc_final: 0.8924 (t0) REVERT: a 332 MET cc_start: 0.9061 (tmm) cc_final: 0.8542 (tmm) REVERT: a 347 ASP cc_start: 0.8477 (p0) cc_final: 0.7952 (p0) REVERT: B 67 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7121 (tm-30) REVERT: B 134 MET cc_start: 0.8588 (tpp) cc_final: 0.7427 (tpp) REVERT: B 192 MET cc_start: 0.8455 (tpp) cc_final: 0.7805 (tpp) REVERT: b 284 MET cc_start: 0.7583 (ptt) cc_final: 0.7368 (mtm) REVERT: b 347 ASP cc_start: 0.7967 (p0) cc_final: 0.7606 (p0) REVERT: H 96 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.8032 (mmm-85) REVERT: L 87 PHE cc_start: 0.8076 (m-80) cc_final: 0.7655 (m-10) REVERT: L 89 LEU cc_start: 0.8657 (tp) cc_final: 0.8321 (tp) REVERT: L 97 ASP cc_start: 0.8884 (t0) cc_final: 0.8424 (t0) REVERT: L 106 GLN cc_start: 0.7984 (pp30) cc_final: 0.7562 (pp30) REVERT: L 120 GLN cc_start: 0.8287 (pm20) cc_final: 0.8086 (pm20) REVERT: C 170 HIS cc_start: 0.6657 (t-90) cc_final: 0.6356 (t-170) REVERT: C 228 GLU cc_start: 0.7994 (pp20) cc_final: 0.7757 (tp30) REVERT: c 361 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8643 (tt) REVERT: c 370 TRP cc_start: 0.7464 (m-10) cc_final: 0.7120 (m-10) outliers start: 19 outliers final: 9 residues processed: 160 average time/residue: 0.0795 time to fit residues: 18.8708 Evaluate side-chains 143 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 361 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 117 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.061547 restraints weight = 37740.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.064049 restraints weight = 20529.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.065791 restraints weight = 14098.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.066996 restraints weight = 10927.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.067813 restraints weight = 9119.815| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11345 Z= 0.128 Angle : 0.733 12.864 15506 Z= 0.339 Chirality : 0.043 0.289 1918 Planarity : 0.003 0.048 1803 Dihedral : 4.893 20.498 1343 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.78 % Allowed : 15.11 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1231 helix: 1.05 (0.27), residues: 377 sheet: 0.83 (0.35), residues: 227 loop : -0.94 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 81 TYR 0.016 0.001 TYR B 219 PHE 0.019 0.002 PHE B 140 TRP 0.012 0.001 TRP B 210 HIS 0.013 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11244) covalent geometry : angle 0.66982 / 0.33 (15226) SS BOND : bond 0.00246 / 0.17 ( 23) SS BOND : angle 0.78316 / 0.51 ( 46) hydrogen bonds : bond 0.03489 / 2.32 ( 447) hydrogen bonds : angle 4.73625 / 3.39 ( 1185) link_ALPHA1-2 : bond 0.00128 / 0.07 ( 2) link_ALPHA1-2 : angle 1.93908 / 1.01 ( 6) link_ALPHA1-3 : bond 0.00525 / 0.25 ( 7) link_ALPHA1-3 : angle 1.81617 / 1.11 ( 21) link_ALPHA1-6 : bond 0.00554 / 0.28 ( 5) link_ALPHA1-6 : angle 1.45354 / 0.87 ( 15) link_BETA1-4 : bond 0.00508 / 0.33 ( 31) link_BETA1-4 : angle 2.03048 / 1.27 ( 93) link_NAG-ASN : bond 0.00503 / 0.31 ( 33) link_NAG-ASN : angle 3.13294 / 1.81 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9020 (ptp) cc_final: 0.8705 (mpp) REVERT: A 134 MET cc_start: 0.9199 (tpp) cc_final: 0.7196 (tpp) REVERT: A 230 HIS cc_start: 0.7629 (m-70) cc_final: 0.7415 (m170) REVERT: a 303 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7518 (tm-30) REVERT: a 311 ASP cc_start: 0.9250 (m-30) cc_final: 0.8920 (t0) REVERT: a 332 MET cc_start: 0.9090 (tmm) cc_final: 0.8569 (tmm) REVERT: a 347 ASP cc_start: 0.8404 (p0) cc_final: 0.8016 (p0) REVERT: a 348 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8434 (mm110) REVERT: B 67 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7226 (tm-30) REVERT: B 134 MET cc_start: 0.8576 (tpp) cc_final: 0.7431 (tpp) REVERT: B 192 MET cc_start: 0.8408 (tpp) cc_final: 0.7873 (tpp) REVERT: B 219 TYR cc_start: 0.8648 (m-80) cc_final: 0.8180 (m-80) REVERT: b 284 MET cc_start: 0.7667 (ptt) cc_final: 0.7453 (mtm) REVERT: b 347 ASP cc_start: 0.7937 (p0) cc_final: 0.7599 (p0) REVERT: L 87 PHE cc_start: 0.8031 (m-80) cc_final: 0.7680 (m-10) REVERT: L 89 LEU cc_start: 0.8612 (tp) cc_final: 0.8272 (tp) REVERT: L 97 ASP cc_start: 0.8849 (t0) cc_final: 0.8396 (t0) REVERT: L 106 GLN cc_start: 0.7954 (pp30) cc_final: 0.7521 (pp30) REVERT: L 120 GLN cc_start: 0.8267 (pm20) cc_final: 0.8047 (pm20) REVERT: C 134 MET cc_start: 0.9398 (tpp) cc_final: 0.9176 (tpp) REVERT: C 170 HIS cc_start: 0.6714 (t-90) cc_final: 0.6443 (t-170) REVERT: c 370 TRP cc_start: 0.7473 (m-10) cc_final: 0.7092 (m-10) outliers start: 20 outliers final: 14 residues processed: 161 average time/residue: 0.0792 time to fit residues: 18.7215 Evaluate side-chains 151 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 0.0370 chunk 89 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.075195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.060072 restraints weight = 37856.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.062516 restraints weight = 20801.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.064191 restraints weight = 14377.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.065359 restraints weight = 11237.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.066197 restraints weight = 9409.460| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11345 Z= 0.167 Angle : 0.762 12.890 15506 Z= 0.354 Chirality : 0.044 0.300 1918 Planarity : 0.003 0.049 1803 Dihedral : 4.908 21.408 1343 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.42 % Allowed : 15.64 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.24), residues: 1231 helix: 1.20 (0.28), residues: 372 sheet: 0.94 (0.35), residues: 219 loop : -1.10 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.017 0.001 TYR B 219 PHE 0.011 0.002 PHE L 87 TRP 0.021 0.002 TRP b 370 HIS 0.014 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (11244) covalent geometry : angle 0.69912 / 0.34 (15226) SS BOND : bond 0.00322 / 0.22 ( 23) SS BOND : angle 1.00951 / 0.67 ( 46) hydrogen bonds : bond 0.03644 / 2.44 ( 447) hydrogen bonds : angle 4.73295 / 3.38 ( 1185) link_ALPHA1-2 : bond 0.00198 / 0.10 ( 2) link_ALPHA1-2 : angle 2.08591 / 1.08 ( 6) link_ALPHA1-3 : bond 0.00485 / 0.22 ( 7) link_ALPHA1-3 : angle 1.78728 / 1.09 ( 21) link_ALPHA1-6 : bond 0.00536 / 0.26 ( 5) link_ALPHA1-6 : angle 1.51608 / 0.90 ( 15) link_BETA1-4 : bond 0.00465 / 0.30 ( 31) link_BETA1-4 : angle 2.06318 / 1.29 ( 93) link_NAG-ASN : bond 0.00472 / 0.29 ( 33) link_NAG-ASN : angle 3.15551 / 1.83 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.287 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: 0.9049 (ptp) cc_final: 0.8721 (mpp) REVERT: A 134 MET cc_start: 0.9268 (tpp) cc_final: 0.7280 (tpp) REVERT: a 303 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7514 (tm-30) REVERT: a 311 ASP cc_start: 0.9286 (m-30) cc_final: 0.9017 (t0) REVERT: a 347 ASP cc_start: 0.8468 (p0) cc_final: 0.7930 (p0) REVERT: B 67 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7292 (tm-30) REVERT: B 134 MET cc_start: 0.8609 (tpp) cc_final: 0.7436 (tpp) REVERT: B 192 MET cc_start: 0.8507 (tpp) cc_final: 0.7945 (tpp) REVERT: b 284 MET cc_start: 0.7759 (ptt) cc_final: 0.7531 (mtm) REVERT: b 347 ASP cc_start: 0.8023 (p0) cc_final: 0.7592 (p0) REVERT: H 96 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.8249 (mmm-85) REVERT: L 87 PHE cc_start: 0.8089 (m-80) cc_final: 0.7810 (m-10) REVERT: L 89 LEU cc_start: 0.8613 (tp) cc_final: 0.8288 (tp) REVERT: L 97 ASP cc_start: 0.8846 (t0) cc_final: 0.8381 (t0) REVERT: L 106 GLN cc_start: 0.8112 (pp30) cc_final: 0.7727 (pp30) REVERT: L 120 GLN cc_start: 0.8219 (pm20) cc_final: 0.7997 (pm20) REVERT: C 170 HIS cc_start: 0.6787 (t-90) cc_final: 0.6471 (t-170) REVERT: c 282 ARG cc_start: 0.7872 (tpt90) cc_final: 0.7394 (tpt90) REVERT: c 370 TRP cc_start: 0.7764 (m-10) cc_final: 0.7313 (m-10) outliers start: 16 outliers final: 10 residues processed: 153 average time/residue: 0.0818 time to fit residues: 18.5337 Evaluate side-chains 146 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 36 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.075238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060154 restraints weight = 37747.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062588 restraints weight = 20773.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064252 restraints weight = 14376.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.065408 restraints weight = 11255.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066242 restraints weight = 9441.579| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11345 Z= 0.160 Angle : 0.759 12.926 15506 Z= 0.353 Chirality : 0.043 0.302 1918 Planarity : 0.004 0.049 1803 Dihedral : 4.917 21.353 1343 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.42 % Allowed : 16.00 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.24), residues: 1231 helix: 1.12 (0.28), residues: 380 sheet: 0.92 (0.35), residues: 219 loop : -1.11 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.016 0.001 TYR B 219 PHE 0.009 0.001 PHE L 87 TRP 0.019 0.002 TRP b 370 HIS 0.014 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (11244) covalent geometry : angle 0.69989 / 0.34 (15226) SS BOND : bond 0.00323 / 0.21 ( 23) SS BOND : angle 0.94683 / 0.62 ( 46) hydrogen bonds : bond 0.03581 / 2.40 ( 447) hydrogen bonds : angle 4.71547 / 3.37 ( 1185) link_ALPHA1-2 : bond 0.00103 / 0.05 ( 2) link_ALPHA1-2 : angle 2.05987 / 1.08 ( 6) link_ALPHA1-3 : bond 0.00497 / 0.22 ( 7) link_ALPHA1-3 : angle 1.77268 / 1.08 ( 21) link_ALPHA1-6 : bond 0.00529 / 0.26 ( 5) link_ALPHA1-6 : angle 1.50104 / 0.89 ( 15) link_BETA1-4 : bond 0.00473 / 0.30 ( 31) link_BETA1-4 : angle 1.96670 / 1.23 ( 93) link_NAG-ASN : bond 0.00466 / 0.29 ( 33) link_NAG-ASN : angle 3.09562 / 1.79 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9291 (tpp) cc_final: 0.7317 (tpp) REVERT: a 303 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7583 (tm-30) REVERT: a 307 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: a 311 ASP cc_start: 0.9319 (m-30) cc_final: 0.9000 (t0) REVERT: a 347 ASP cc_start: 0.8427 (p0) cc_final: 0.7900 (p0) REVERT: B 67 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7305 (tm-30) REVERT: B 134 MET cc_start: 0.8586 (tpp) cc_final: 0.7427 (tpp) REVERT: B 192 MET cc_start: 0.8530 (tpp) cc_final: 0.7980 (tpp) REVERT: b 284 MET cc_start: 0.7829 (ptt) cc_final: 0.7571 (mtm) REVERT: b 347 ASP cc_start: 0.8004 (p0) cc_final: 0.7643 (p0) REVERT: H 48 LYS cc_start: 0.8134 (tptt) cc_final: 0.7913 (tptt) REVERT: L 87 PHE cc_start: 0.8182 (m-80) cc_final: 0.7923 (m-10) REVERT: L 89 LEU cc_start: 0.8608 (tp) cc_final: 0.8279 (tp) REVERT: L 97 ASP cc_start: 0.8910 (t0) cc_final: 0.8450 (t0) REVERT: L 106 GLN cc_start: 0.8117 (pp30) cc_final: 0.7736 (pp30) REVERT: L 120 GLN cc_start: 0.8226 (pm20) cc_final: 0.7976 (pm20) REVERT: C 170 HIS cc_start: 0.6812 (t-90) cc_final: 0.6512 (t-170) REVERT: c 282 ARG cc_start: 0.7915 (tpt90) cc_final: 0.7428 (tpt90) REVERT: c 300 LYS cc_start: 0.9296 (mmmm) cc_final: 0.8960 (mtmm) REVERT: c 370 TRP cc_start: 0.7763 (m-10) cc_final: 0.7232 (m-90) outliers start: 16 outliers final: 13 residues processed: 151 average time/residue: 0.0782 time to fit residues: 17.3965 Evaluate side-chains 149 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 307 GLU Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.061305 restraints weight = 37023.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.063821 restraints weight = 19712.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065527 restraints weight = 13346.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066722 restraints weight = 10284.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.067571 restraints weight = 8518.432| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11345 Z= 0.134 Angle : 0.740 12.852 15506 Z= 0.345 Chirality : 0.043 0.301 1918 Planarity : 0.004 0.051 1803 Dihedral : 4.851 21.097 1343 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 1.42 % Allowed : 16.00 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1231 helix: 1.17 (0.28), residues: 375 sheet: 0.95 (0.36), residues: 219 loop : -1.12 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.016 0.001 TYR B 219 PHE 0.010 0.001 PHE B 140 TRP 0.018 0.001 TRP b 370 HIS 0.015 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (11244) covalent geometry : angle 0.68364 / 0.33 (15226) SS BOND : bond 0.00270 / 0.18 ( 23) SS BOND : angle 0.81020 / 0.52 ( 46) hydrogen bonds : bond 0.03362 / 2.26 ( 447) hydrogen bonds : angle 4.67611 / 3.34 ( 1185) link_ALPHA1-2 : bond 0.00161 / 0.08 ( 2) link_ALPHA1-2 : angle 1.98219 / 1.03 ( 6) link_ALPHA1-3 : bond 0.00480 / 0.22 ( 7) link_ALPHA1-3 : angle 1.80988 / 1.12 ( 21) link_ALPHA1-6 : bond 0.00526 / 0.27 ( 5) link_ALPHA1-6 : angle 1.46895 / 0.87 ( 15) link_BETA1-4 : bond 0.00493 / 0.32 ( 31) link_BETA1-4 : angle 1.87852 / 1.18 ( 93) link_NAG-ASN : bond 0.00478 / 0.29 ( 33) link_NAG-ASN : angle 3.00441 / 1.74 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9283 (tpp) cc_final: 0.7285 (tpp) REVERT: a 303 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7534 (tm-30) REVERT: a 311 ASP cc_start: 0.9300 (m-30) cc_final: 0.8990 (t70) REVERT: a 347 ASP cc_start: 0.8416 (p0) cc_final: 0.7867 (p0) REVERT: a 353 ASN cc_start: 0.9140 (m-40) cc_final: 0.8850 (t0) REVERT: B 67 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7343 (tm-30) REVERT: B 134 MET cc_start: 0.8581 (tpp) cc_final: 0.7426 (tpp) REVERT: B 192 MET cc_start: 0.8530 (tpp) cc_final: 0.7980 (tpp) REVERT: B 219 TYR cc_start: 0.8579 (m-80) cc_final: 0.7702 (m-80) REVERT: b 347 ASP cc_start: 0.8059 (p0) cc_final: 0.7620 (p0) REVERT: H 48 LYS cc_start: 0.8138 (tptt) cc_final: 0.7923 (tptt) REVERT: H 96 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8209 (mmm-85) REVERT: L 87 PHE cc_start: 0.8136 (m-80) cc_final: 0.7899 (m-10) REVERT: L 89 LEU cc_start: 0.8607 (tp) cc_final: 0.8238 (tp) REVERT: L 97 ASP cc_start: 0.8875 (t0) cc_final: 0.8413 (t0) REVERT: L 106 GLN cc_start: 0.8036 (pp30) cc_final: 0.7642 (pp30) REVERT: C 170 HIS cc_start: 0.6802 (t-90) cc_final: 0.6513 (t-170) REVERT: c 300 LYS cc_start: 0.9274 (mmmm) cc_final: 0.8998 (mtmm) REVERT: c 370 TRP cc_start: 0.7721 (m-10) cc_final: 0.7174 (m-90) outliers start: 16 outliers final: 11 residues processed: 155 average time/residue: 0.0871 time to fit residues: 19.9343 Evaluate side-chains 148 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 117 optimal weight: 0.0770 chunk 56 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.061350 restraints weight = 38006.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.063795 restraints weight = 21012.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.065486 restraints weight = 14596.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.066666 restraints weight = 11429.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067500 restraints weight = 9595.576| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11345 Z= 0.131 Angle : 0.741 12.777 15506 Z= 0.347 Chirality : 0.043 0.298 1918 Planarity : 0.004 0.051 1803 Dihedral : 4.849 20.936 1343 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 0.98 % Allowed : 16.53 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1231 helix: 1.14 (0.27), residues: 380 sheet: 0.94 (0.36), residues: 219 loop : -1.05 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.016 0.001 TYR B 219 PHE 0.010 0.001 PHE B 140 TRP 0.022 0.002 TRP C 227 HIS 0.016 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11244) covalent geometry : angle 0.68721 / 0.34 (15226) SS BOND : bond 0.00255 / 0.18 ( 23) SS BOND : angle 0.76427 / 0.47 ( 46) hydrogen bonds : bond 0.03307 / 2.19 ( 447) hydrogen bonds : angle 4.63922 / 3.32 ( 1185) link_ALPHA1-2 : bond 0.00144 / 0.08 ( 2) link_ALPHA1-2 : angle 1.97264 / 1.03 ( 6) link_ALPHA1-3 : bond 0.00491 / 0.23 ( 7) link_ALPHA1-3 : angle 1.73352 / 1.06 ( 21) link_ALPHA1-6 : bond 0.00526 / 0.27 ( 5) link_ALPHA1-6 : angle 1.45190 / 0.87 ( 15) link_BETA1-4 : bond 0.00479 / 0.31 ( 31) link_BETA1-4 : angle 1.83338 / 1.15 ( 93) link_NAG-ASN : bond 0.00483 / 0.29 ( 33) link_NAG-ASN : angle 2.95521 / 1.71 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1384.13 seconds wall clock time: 24 minutes 58.64 seconds (1498.64 seconds total)