Starting phenix.real_space_refine on Tue Aug 26 07:04:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvz_39617/08_2025/8yvz_39617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvz_39617/08_2025/8yvz_39617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yvz_39617/08_2025/8yvz_39617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvz_39617/08_2025/8yvz_39617.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yvz_39617/08_2025/8yvz_39617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvz_39617/08_2025/8yvz_39617.map" } resolution = 3.45 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= 0.011 sd= 0.099 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 296 5.16 5 C 21800 2.51 5 N 5996 2.21 5 O 6644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34740 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "D" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "F" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "G" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "H" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "I" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "J" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 386} Chain: "K" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "L" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "M" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "N" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "P" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "Q" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "E" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 328 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "R" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 328 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "S" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 328 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "T" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 328 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.30, per 1000 atoms: 0.21 Number of scatterers: 34740 At special positions: 0 Unit cell: (218.16, 179.28, 218.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 296 16.00 O 6644 8.00 N 5996 7.00 C 21800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=68, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 18 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 27 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.05 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.03 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.05 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 259 " - pdb=" SG CYS H 271 " distance=2.05 Simple disulfide: pdb=" SG CYS H 301 " - pdb=" SG CYS H 376 " distance=2.03 Simple disulfide: pdb=" SG CYS H 306 " - pdb=" SG CYS H 380 " distance=2.03 Simple disulfide: pdb=" SG CYS H 328 " - pdb=" SG CYS H 370 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 125 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 105 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 225 " distance=2.03 Simple disulfide: pdb=" SG CYS I 203 " - pdb=" SG CYS I 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 125 " distance=2.03 Simple disulfide: pdb=" SG CYS J 91 " - pdb=" SG CYS J 105 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 225 " distance=2.03 Simple disulfide: pdb=" SG CYS J 203 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 125 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 225 " distance=2.03 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS L 9 " - pdb=" SG CYS L 18 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 27 " distance=2.03 Simple disulfide: pdb=" SG CYS L 26 " - pdb=" SG CYS L 58 " distance=2.03 Simple disulfide: pdb=" SG CYS M 9 " - pdb=" SG CYS M 18 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 27 " distance=2.03 Simple disulfide: pdb=" SG CYS M 26 " - pdb=" SG CYS M 58 " distance=2.03 Simple disulfide: pdb=" SG CYS N 9 " - pdb=" SG CYS N 18 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 26 " - pdb=" SG CYS N 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 120 " - pdb=" SG CYS E 140 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 120 " - pdb=" SG CYS R 140 " distance=2.03 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 149 " distance=2.03 Simple disulfide: pdb=" SG CYS S 113 " - pdb=" SG CYS S 127 " distance=2.03 Simple disulfide: pdb=" SG CYS S 120 " - pdb=" SG CYS S 140 " distance=2.03 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 149 " distance=2.03 Simple disulfide: pdb=" SG CYS T 113 " - pdb=" SG CYS T 127 " distance=2.03 Simple disulfide: pdb=" SG CYS T 120 " - pdb=" SG CYS T 140 " distance=2.03 Simple disulfide: pdb=" SG CYS T 134 " - pdb=" SG CYS T 149 " distance=2.03 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 BETA1-4 " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " NAG-ASN " NAG U 1 " - " ASN A 141 " " NAG V 1 " - " ASN B 262 " " NAG W 1 " - " ASN B 200 " " NAG X 1 " - " ASN F 141 " " NAG Y 1 " - " ASN G 141 " " NAG Z 1 " - " ASN H 141 " " NAG a 1 " - " ASN I 262 " " NAG b 1 " - " ASN I 200 " " NAG c 1 " - " ASN J 262 " " NAG d 1 " - " ASN J 200 " " NAG e 1 " - " ASN K 262 " " NAG f 1 " - " ASN K 200 " Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8256 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 80 sheets defined 15.9% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.893A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.073A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.581A pdb=" N PHE A 287 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 438 Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 350 through 361 removed outlier: 3.620A pdb=" N VAL B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN B 356 " --> pdb=" O HIS B 352 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 397 removed outlier: 4.009A pdb=" N SER B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 401 Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.725A pdb=" N ILE B 413 " --> pdb=" O TRP B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 31 through 41 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.550A pdb=" N MET D 177 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 removed outlier: 3.669A pdb=" N TYR F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 4.105A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 259' Processing helix chain 'F' and resid 404 through 438 removed outlier: 3.696A pdb=" N ARG F 438 " --> pdb=" O ILE F 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.652A pdb=" N TYR G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.207A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 255 through 259' Processing helix chain 'G' and resid 283 through 287 removed outlier: 3.555A pdb=" N ALA G 286 " --> pdb=" O PRO G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 438 Processing helix chain 'H' and resid 238 through 247 removed outlier: 3.543A pdb=" N TYR H 242 " --> pdb=" O SER H 238 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 259 removed outlier: 4.012A pdb=" N GLY H 258 " --> pdb=" O ALA H 255 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS H 259 " --> pdb=" O PRO H 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 255 through 259' Processing helix chain 'H' and resid 404 through 438 removed outlier: 3.511A pdb=" N ARG H 438 " --> pdb=" O ILE H 434 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 removed outlier: 4.121A pdb=" N THR I 205 " --> pdb=" O THR I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 225 removed outlier: 3.787A pdb=" N GLN I 224 " --> pdb=" O LEU I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 361 removed outlier: 3.611A pdb=" N VAL I 355 " --> pdb=" O PRO I 351 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN I 356 " --> pdb=" O HIS I 352 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU I 361 " --> pdb=" O TYR I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 397 removed outlier: 4.146A pdb=" N SER I 368 " --> pdb=" O ALA I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 401 removed outlier: 3.588A pdb=" N LEU I 401 " --> pdb=" O PRO I 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 398 through 401' Processing helix chain 'I' and resid 407 through 414 removed outlier: 3.526A pdb=" N ILE I 413 " --> pdb=" O TRP I 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 12 removed outlier: 3.798A pdb=" N ALA J 11 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR J 12 " --> pdb=" O TYR J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 361 removed outlier: 3.659A pdb=" N VAL J 355 " --> pdb=" O PRO J 351 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN J 356 " --> pdb=" O HIS J 352 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU J 361 " --> pdb=" O TYR J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 396 Processing helix chain 'J' and resid 397 through 401 Processing helix chain 'J' and resid 407 through 414 removed outlier: 3.706A pdb=" N ILE J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 11 Processing helix chain 'K' and resid 350 through 361 removed outlier: 3.645A pdb=" N VAL K 355 " --> pdb=" O PRO K 351 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN K 356 " --> pdb=" O HIS K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 397 Processing helix chain 'K' and resid 398 through 402 removed outlier: 3.895A pdb=" N THR K 402 " --> pdb=" O TYR K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 407 through 414 removed outlier: 3.669A pdb=" N ILE K 413 " --> pdb=" O TRP K 409 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 31 Processing helix chain 'L' and resid 31 through 40 Processing helix chain 'L' and resid 48 through 56 removed outlier: 3.515A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 31 Processing helix chain 'M' and resid 31 through 42 Processing helix chain 'M' and resid 47 through 56 Processing helix chain 'N' and resid 26 through 31 Processing helix chain 'N' and resid 31 through 41 Processing helix chain 'N' and resid 47 through 55 Processing helix chain 'O' and resid 108 through 119 Processing helix chain 'O' and resid 152 through 158 removed outlier: 3.771A pdb=" N LYS O 157 " --> pdb=" O ALA O 153 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU O 158 " --> pdb=" O ASP O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 181 removed outlier: 4.507A pdb=" N SER O 179 " --> pdb=" O HIS O 176 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA O 181 " --> pdb=" O ARG O 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 119 Processing helix chain 'P' and resid 152 through 157 removed outlier: 3.905A pdb=" N LYS P 157 " --> pdb=" O ALA P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 181 removed outlier: 5.014A pdb=" N SER P 179 " --> pdb=" O HIS P 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA P 181 " --> pdb=" O ARG P 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 119 Processing helix chain 'Q' and resid 152 through 157 removed outlier: 3.623A pdb=" N LYS Q 157 " --> pdb=" O ALA Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 178 removed outlier: 3.525A pdb=" N MET Q 177 " --> pdb=" O PRO Q 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'R' and resid 129 through 133 Processing helix chain 'R' and resid 143 through 147 Processing helix chain 'S' and resid 129 through 133 Processing helix chain 'S' and resid 143 through 147 Processing helix chain 'T' and resid 129 through 133 Processing helix chain 'T' and resid 143 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 27 through 42 current: chain 'A' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 143 through 147 current: chain 'A' and resid 183 through 186 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 101 through 110 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA5, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 262 removed outlier: 3.594A pdb=" N ARG A 267 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 296 through 306 removed outlier: 5.731A pdb=" N ASP A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS A 321 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA9, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.626A pdb=" N ALA B 17 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS B 19 " --> pdb=" O CYS B 28 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS B 28 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 79 removed outlier: 4.587A pdb=" N GLY B 55 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N THR B 65 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 11.778A pdb=" N GLN B 53 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 11.739A pdb=" N ILE B 67 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 11.465A pdb=" N SER B 51 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 13.113A pdb=" N TYR B 69 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 16.512A pdb=" N GLN B 49 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N PHE B 50 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 11.841A pdb=" N LEU B 102 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N ALA B 52 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE B 100 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE B 56 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 13.090A pdb=" N THR B 96 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 84 through 86 removed outlier: 5.459A pdb=" N TYR B 129 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLN B 112 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE B 127 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N SER B 114 " --> pdb=" O CYS B 125 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N CYS B 125 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN B 116 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ARG B 123 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 149 through 156 Processing sheet with id=AB5, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.552A pdb=" N GLY B 209 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'B' and resid 274 through 277 Processing sheet with id=AB8, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.583A pdb=" N VAL D 149 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 131 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS D 125 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL D 129 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N TYR D 132 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 191 through 195 removed outlier: 3.829A pdb=" N GLY D 191 " --> pdb=" O TYR D 202 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 206 through 209 current: chain 'D' and resid 230 through 240 removed outlier: 7.833A pdb=" N ALA D 232 " --> pdb=" O TRP D 251 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N TRP D 251 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL D 234 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 249 " --> pdb=" O VAL D 234 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 2 through 8 removed outlier: 3.629A pdb=" N HIS F 3 " --> pdb=" O MET F 280 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 27 through 42 current: chain 'F' and resid 119 through 136 removed outlier: 3.545A pdb=" N VAL F 146 " --> pdb=" O ALA F 131 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 143 through 147 current: chain 'F' and resid 183 through 185 Processing sheet with id=AC3, first strand: chain 'F' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 51 through 54 current: chain 'F' and resid 100 through 110 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AC5, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AC6, first strand: chain 'F' and resid 260 through 262 removed outlier: 3.650A pdb=" N ARG F 267 " --> pdb=" O LYS F 262 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 296 through 305 removed outlier: 5.695A pdb=" N ASP F 298 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS F 321 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL F 315 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 326 through 328 Processing sheet with id=AC9, first strand: chain 'F' and resid 331 through 332 Processing sheet with id=AD1, first strand: chain 'F' and resid 387 through 388 removed outlier: 3.596A pdb=" N HIS I 306 " --> pdb=" O TYR I 296 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AD3, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.349A pdb=" N MET G 31 " --> pdb=" O MET G 136 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE G 47 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 140 through 147 current: chain 'G' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 183 through 186 current: chain 'G' and resid 267 through 269 Processing sheet with id=AD4, first strand: chain 'G' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 54 current: chain 'G' and resid 100 through 110 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AD6, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AD7, first strand: chain 'G' and resid 297 through 306 removed outlier: 5.754A pdb=" N ASP G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS G 321 " --> pdb=" O ASP G 298 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL G 315 " --> pdb=" O ALA G 304 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AD9, first strand: chain 'G' and resid 387 through 388 removed outlier: 3.507A pdb=" N HIS J 306 " --> pdb=" O TYR J 296 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 2 through 8 Processing sheet with id=AE2, first strand: chain 'H' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 27 through 42 current: chain 'H' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 140 through 147 current: chain 'H' and resid 183 through 185 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 183 through 185 current: chain 'H' and resid 267 through 269 Processing sheet with id=AE3, first strand: chain 'H' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 51 through 54 current: chain 'H' and resid 101 through 110 No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AE5, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AE6, first strand: chain 'H' and resid 296 through 305 removed outlier: 5.591A pdb=" N ASP H 298 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS H 321 " --> pdb=" O ASP H 298 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL H 315 " --> pdb=" O ALA H 304 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 326 through 328 removed outlier: 3.589A pdb=" N GLY H 326 " --> pdb=" O VAL H 346 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA H 344 " --> pdb=" O CYS H 328 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 331 through 332 Processing sheet with id=AE9, first strand: chain 'H' and resid 387 through 388 Processing sheet with id=AF1, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AF2, first strand: chain 'I' and resid 46 through 54 removed outlier: 11.039A pdb=" N PHE I 50 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 11.472A pdb=" N LEU I 102 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 9.828A pdb=" N ALA I 52 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE I 100 " --> pdb=" O ALA I 52 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 66 through 70 Processing sheet with id=AF4, first strand: chain 'I' and resid 84 through 86 removed outlier: 4.088A pdb=" N GLU I 109 " --> pdb=" O TYR I 129 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE I 115 " --> pdb=" O ARG I 123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 149 through 156 removed outlier: 3.583A pdb=" N VAL I 267 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 175 through 177 removed outlier: 3.882A pdb=" N VAL I 227 " --> pdb=" O ASP I 177 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AF8, first strand: chain 'I' and resid 198 through 200 removed outlier: 3.836A pdb=" N GLY I 209 " --> pdb=" O TYR I 199 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 274 through 277 Processing sheet with id=AG1, first strand: chain 'J' and resid 17 through 19 removed outlier: 3.605A pdb=" N CYS J 19 " --> pdb=" O CYS J 28 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS J 28 " --> pdb=" O CYS J 19 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 49 through 54 removed outlier: 6.091A pdb=" N HIS J 99 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ALA J 52 " --> pdb=" O MET J 97 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N MET J 97 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N ILE J 54 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N GLY J 95 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 66 through 70 Processing sheet with id=AG4, first strand: chain 'J' and resid 84 through 86 removed outlier: 5.454A pdb=" N TYR J 129 " --> pdb=" O PHE J 110 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLN J 112 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE J 127 " --> pdb=" O GLN J 112 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N SER J 114 " --> pdb=" O CYS J 125 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N CYS J 125 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLN J 116 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG J 123 " --> pdb=" O GLN J 116 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 149 through 152 Processing sheet with id=AG6, first strand: chain 'J' and resid 155 through 156 Processing sheet with id=AG7, first strand: chain 'J' and resid 167 through 169 Processing sheet with id=AG8, first strand: chain 'J' and resid 175 through 176 removed outlier: 3.505A pdb=" N VAL J 197 " --> pdb=" O THR J 211 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY J 209 " --> pdb=" O TYR J 199 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 181 through 183 Processing sheet with id=AH1, first strand: chain 'J' and resid 274 through 277 Processing sheet with id=AH2, first strand: chain 'K' and resid 17 through 18 Processing sheet with id=AH3, first strand: chain 'K' and resid 49 through 54 removed outlier: 11.428A pdb=" N PHE K 50 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 11.699A pdb=" N LEU K 102 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N ALA K 52 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE K 100 " --> pdb=" O ALA K 52 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 66 through 69 Processing sheet with id=AH5, first strand: chain 'K' and resid 84 through 86 removed outlier: 4.218A pdb=" N GLU K 109 " --> pdb=" O TYR K 129 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL K 113 " --> pdb=" O CYS K 125 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 149 through 152 Processing sheet with id=AH7, first strand: chain 'K' and resid 155 through 156 Processing sheet with id=AH8, first strand: chain 'K' and resid 175 through 176 removed outlier: 3.639A pdb=" N TYR K 199 " --> pdb=" O GLY K 209 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY K 209 " --> pdb=" O TYR K 199 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 182 through 183 Processing sheet with id=AI1, first strand: chain 'K' and resid 274 through 277 Processing sheet with id=AI2, first strand: chain 'O' and resid 139 through 141 removed outlier: 5.342A pdb=" N VAL O 129 " --> pdb=" O HIS O 125 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N HIS O 125 " --> pdb=" O VAL O 129 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 161 through 163 removed outlier: 3.504A pdb=" N LEU O 168 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'O' and resid 191 through 195 removed outlier: 3.653A pdb=" N GLY O 191 " --> pdb=" O TYR O 202 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 206 through 209 current: chain 'O' and resid 230 through 240 removed outlier: 7.400A pdb=" N ALA O 232 " --> pdb=" O TRP O 251 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N TRP O 251 " --> pdb=" O ALA O 232 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL O 234 " --> pdb=" O VAL O 249 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL O 249 " --> pdb=" O VAL O 234 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR O 257 " --> pdb=" O THR O 250 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 149 through 150 removed outlier: 4.062A pdb=" N GLY P 131 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS P 125 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL P 129 " --> pdb=" O HIS P 125 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N TYR P 132 " --> pdb=" O PRO P 143 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU P 168 " --> pdb=" O SER P 163 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'P' and resid 191 through 195 removed outlier: 3.580A pdb=" N GLY P 191 " --> pdb=" O TYR P 202 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 206 through 209 current: chain 'P' and resid 230 through 240 removed outlier: 7.924A pdb=" N ALA P 232 " --> pdb=" O TRP P 251 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TRP P 251 " --> pdb=" O ALA P 232 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL P 234 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL P 249 " --> pdb=" O VAL P 234 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.574A pdb=" N VAL Q 149 " --> pdb=" O LYS Q 124 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE Q 121 " --> pdb=" O TYR Q 132 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR Q 132 " --> pdb=" O PHE Q 121 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL Q 123 " --> pdb=" O THR Q 130 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N TYR Q 132 " --> pdb=" O PRO Q 143 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU Q 168 " --> pdb=" O SER Q 163 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER Q 163 " --> pdb=" O LEU Q 168 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 191 through 195 removed outlier: 3.523A pdb=" N GLY Q 198 " --> pdb=" O TRP Q 195 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 207 through 209 current: chain 'Q' and resid 230 through 240 removed outlier: 7.695A pdb=" N ALA Q 232 " --> pdb=" O TRP Q 251 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N TRP Q 251 " --> pdb=" O ALA Q 232 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL Q 234 " --> pdb=" O VAL Q 249 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL Q 249 " --> pdb=" O VAL Q 234 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2529 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: 6.83 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11333 1.35 - 1.46: 8512 1.46 - 1.58: 15379 1.58 - 1.70: 0 1.70 - 1.82: 396 Bond restraints: 35620 Sorted by residual: bond pdb=" C1 BMA Y 3 " pdb=" C2 BMA Y 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1 BMA d 3 " pdb=" C2 BMA d 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C1 BMA b 3 " pdb=" C2 BMA b 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C1 BMA V 3 " pdb=" C2 BMA V 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C1 BMA f 3 " pdb=" C2 BMA f 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.48e+00 ... (remaining 35615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 47805 2.36 - 4.71: 602 4.71 - 7.07: 69 7.07 - 9.43: 8 9.43 - 11.78: 4 Bond angle restraints: 48488 Sorted by residual: angle pdb=" CA PRO K 398 " pdb=" N PRO K 398 " pdb=" CD PRO K 398 " ideal model delta sigma weight residual 112.00 103.71 8.29 1.40e+00 5.10e-01 3.50e+01 angle pdb=" N ILE T 118 " pdb=" CA ILE T 118 " pdb=" C ILE T 118 " ideal model delta sigma weight residual 113.47 107.91 5.56 1.01e+00 9.80e-01 3.03e+01 angle pdb=" N ILE S 118 " pdb=" CA ILE S 118 " pdb=" C ILE S 118 " ideal model delta sigma weight residual 113.10 108.89 4.21 9.70e-01 1.06e+00 1.89e+01 angle pdb=" N ARG R 114 " pdb=" CA ARG R 114 " pdb=" C ARG R 114 " ideal model delta sigma weight residual 108.19 113.71 -5.52 1.29e+00 6.01e-01 1.83e+01 angle pdb=" N ARG S 114 " pdb=" CA ARG S 114 " pdb=" C ARG S 114 " ideal model delta sigma weight residual 108.34 113.88 -5.54 1.31e+00 5.83e-01 1.79e+01 ... (remaining 48483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.26: 20393 22.26 - 44.52: 1242 44.52 - 66.78: 132 66.78 - 89.03: 102 89.03 - 111.29: 51 Dihedral angle restraints: 21920 sinusoidal: 9044 harmonic: 12876 Sorted by residual: dihedral pdb=" CB CYS T 120 " pdb=" SG CYS T 120 " pdb=" SG CYS T 140 " pdb=" CB CYS T 140 " ideal model delta sinusoidal sigma weight residual -86.00 -165.58 79.58 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CB CYS S 120 " pdb=" SG CYS S 120 " pdb=" SG CYS S 140 " pdb=" CB CYS S 140 " ideal model delta sinusoidal sigma weight residual -86.00 -165.12 79.12 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CB CYS E 120 " pdb=" SG CYS E 120 " pdb=" SG CYS E 140 " pdb=" CB CYS E 140 " ideal model delta sinusoidal sigma weight residual -86.00 -163.67 77.67 1 1.00e+01 1.00e-02 7.55e+01 ... (remaining 21917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4824 0.071 - 0.142: 616 0.142 - 0.214: 22 0.214 - 0.285: 12 0.285 - 0.356: 2 Chirality restraints: 5476 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN J 262 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C1 NAG e 1 " pdb=" ND2 ASN K 262 " pdb=" C2 NAG e 1 " pdb=" O5 NAG e 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 5473 not shown) Planarity restraints: 6256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 397 " -0.087 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO K 398 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO K 398 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO K 398 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 350 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO B 351 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 351 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 351 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 21 " 0.048 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO A 22 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.040 5.00e-02 4.00e+02 ... (remaining 6253 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1287 2.72 - 3.26: 32895 3.26 - 3.81: 52063 3.81 - 4.35: 61726 4.35 - 4.90: 110796 Nonbonded interactions: 258767 Sorted by model distance: nonbonded pdb=" OH TYR B 69 " pdb=" OD1 ASP B 117 " model vdw 2.169 3.040 nonbonded pdb=" OD1 ASP F 311 " pdb=" N PHE F 312 " model vdw 2.180 3.120 nonbonded pdb=" OG1 THR F 300 " pdb=" OG1 THR F 319 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR H 300 " pdb=" OG1 THR H 319 " model vdw 2.216 3.040 nonbonded pdb=" O TYR I 358 " pdb=" OG1 THR I 366 " model vdw 2.226 3.040 ... (remaining 258762 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.570 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5369 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 : 0.004 0.075 35724 Z= 0.164 Angle : 0.641 11.785 48732 Z= 0.322 Chirality : 0.047 0.356 5476 Planarity : 0.005 0.126 6244 Dihedral : 15.734 111.293 13460 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.87 % Favored : 92.93 % Rotamer: Outliers : 0.08 % Allowed : 0.29 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.13), residues: 4412 helix: 3.20 (0.24), residues: 484 sheet: -0.86 (0.15), residues: 1208 loop : -1.41 (0.12), residues: 2720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 115 TYR 0.022 0.001 TYR B 305 PHE 0.025 0.001 PHE J 50 TRP 0.011 0.001 TRP J 329 HIS 0.007 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00372 (35620) covalent geometry : angle 0.62775 (48488) SS BOND : bond 0.00432 ( 68) SS BOND : angle 1.12527 ( 136) hydrogen bonds : bond 0.22389 ( 991) hydrogen bonds : angle 8.06298 ( 2529) link_BETA1-4 : bond 0.00851 ( 24) link_BETA1-4 : angle 2.67470 ( 72) link_NAG-ASN : bond 0.00348 ( 12) link_NAG-ASN : angle 2.47683 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 948 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 ILE cc_start: 0.6365 (mm) cc_final: 0.6048 (mm) REVERT: D 177 MET cc_start: 0.7099 (mpp) cc_final: 0.6389 (mtm) REVERT: D 194 ASN cc_start: 0.7319 (m110) cc_final: 0.7087 (m110) REVERT: D 202 TYR cc_start: 0.7125 (t80) cc_final: 0.6474 (t80) REVERT: H 402 MET cc_start: 0.6563 (mmt) cc_final: 0.6346 (tpp) REVERT: I 246 ASP cc_start: 0.6882 (p0) cc_final: 0.6632 (t0) REVERT: J 127 ILE cc_start: 0.5201 (tt) cc_final: 0.4896 (tt) REVERT: J 297 ARG cc_start: 0.4218 (ptt90) cc_final: 0.3663 (ptt180) REVERT: K 215 MET cc_start: 0.6050 (mtp) cc_final: 0.5720 (mtm) REVERT: O 128 LYS cc_start: 0.7427 (ptpp) cc_final: 0.7123 (ptmt) REVERT: P 113 MET cc_start: 0.6978 (mmt) cc_final: 0.6769 (mmt) REVERT: P 147 LYS cc_start: 0.5800 (ptpp) cc_final: 0.5460 (mttt) REVERT: R 110 MET cc_start: 0.1346 (ptp) cc_final: -0.0334 (ttp) REVERT: S 110 MET cc_start: 0.2593 (ppp) cc_final: 0.1574 (pmm) REVERT: T 132 TRP cc_start: 0.5559 (m-10) cc_final: 0.5310 (m-10) outliers start: 3 outliers final: 0 residues processed: 949 average time/residue: 0.1962 time to fit residues: 301.3384 Evaluate side-chains 583 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS B 255 HIS B 304 GLN B 340 GLN C 30 ASN F 386 HIS G 3 HIS G 187 GLN G 235 GLN G 252 ASN I 131 HIS I 255 HIS I 352 HIS J 232 HIS J 306 HIS J 340 GLN K 131 HIS K 212 ASN K 226 HIS K 277 HIS ** O 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 ASN Q 172 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130761 restraints weight = 47193.931| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.24 r_work: 0.3331 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 35724 Z= 0.143 Angle : 0.702 12.017 48732 Z= 0.345 Chirality : 0.047 0.264 5476 Planarity : 0.005 0.067 6244 Dihedral : 9.030 69.062 5548 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.07 % Favored : 93.74 % Rotamer: Outliers : 2.70 % Allowed : 10.13 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.13), residues: 4412 helix: 2.25 (0.22), residues: 552 sheet: -0.71 (0.14), residues: 1236 loop : -1.36 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 178 TYR 0.042 0.002 TYR A 93 PHE 0.024 0.001 PHE K 110 TRP 0.019 0.001 TRP J 329 HIS 0.010 0.001 HIS G 3 Details of bonding type rmsd covalent geometry : bond 0.00316 (35620) covalent geometry : angle 0.68167 (48488) SS BOND : bond 0.00355 ( 68) SS BOND : angle 1.21105 ( 136) hydrogen bonds : bond 0.03614 ( 991) hydrogen bonds : angle 5.81004 ( 2529) link_BETA1-4 : bond 0.00963 ( 24) link_BETA1-4 : angle 3.44594 ( 72) link_NAG-ASN : bond 0.01316 ( 12) link_NAG-ASN : angle 3.34261 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 670 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 TYR cc_start: 0.6896 (t80) cc_final: 0.6227 (t80) REVERT: A 228 MET cc_start: 0.4981 (tpp) cc_final: 0.4570 (mpp) REVERT: B 151 ILE cc_start: 0.6950 (mm) cc_final: 0.6727 (mm) REVERT: B 373 MET cc_start: 0.6413 (mmt) cc_final: 0.5434 (mtt) REVERT: C 8 MET cc_start: 0.5270 (mpp) cc_final: 0.4661 (mpp) REVERT: D 124 LYS cc_start: 0.8349 (pttt) cc_final: 0.7770 (mtmm) REVERT: D 230 VAL cc_start: 0.5667 (t) cc_final: 0.5321 (p) REVERT: G 51 TYR cc_start: 0.6776 (p90) cc_final: 0.6534 (p90) REVERT: G 77 GLN cc_start: 0.6871 (mm-40) cc_final: 0.6599 (mm-40) REVERT: H 245 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6431 (mppt) REVERT: H 402 MET cc_start: 0.6876 (mmt) cc_final: 0.6625 (tpp) REVERT: I 226 HIS cc_start: 0.5334 (m170) cc_final: 0.5131 (t-170) REVERT: I 246 ASP cc_start: 0.7189 (p0) cc_final: 0.6705 (t0) REVERT: J 97 MET cc_start: 0.7122 (mmm) cc_final: 0.6810 (tpt) REVERT: K 210 THR cc_start: 0.8582 (t) cc_final: 0.8192 (p) REVERT: K 269 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6163 (mtm) REVERT: K 287 HIS cc_start: 0.5732 (OUTLIER) cc_final: 0.5520 (t-90) REVERT: O 201 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.6457 (pm20) REVERT: P 113 MET cc_start: 0.7345 (mmt) cc_final: 0.7124 (mmt) REVERT: Q 152 ASN cc_start: 0.7416 (t0) cc_final: 0.7189 (t0) REVERT: R 110 MET cc_start: 0.2065 (ptp) cc_final: 0.0345 (ttm) REVERT: S 110 MET cc_start: 0.3505 (ppp) cc_final: 0.2858 (pmm) REVERT: T 132 TRP cc_start: 0.5476 (m-10) cc_final: 0.5119 (m-10) outliers start: 102 outliers final: 59 residues processed: 728 average time/residue: 0.1791 time to fit residues: 220.4088 Evaluate side-chains 633 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 570 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 134 GLN Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 329 TRP Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 287 HIS Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 333 ASP Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 42 ASN Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain O residue 124 LYS Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 201 GLN Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 244 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 219 optimal weight: 0.0870 chunk 6 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 424 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 204 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 402 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 412 optimal weight: 8.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS B 304 GLN D 201 GLN F 43 ASN F 175 ASN F 394 HIS G 3 HIS ** G 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS H 308 HIS H 394 HIS I 53 GLN I 255 HIS I 331 ASN J 53 GLN ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 HIS K 7 ASN K 77 ASN K 99 HIS K 212 ASN K 226 HIS K 328 HIS O 197 HIS O 252 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.174941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129131 restraints weight = 47584.459| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.34 r_work: 0.3319 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 35724 Z= 0.177 Angle : 0.667 12.482 48732 Z= 0.335 Chirality : 0.046 0.254 5476 Planarity : 0.005 0.092 6244 Dihedral : 6.422 57.411 5548 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.94 % Favored : 93.86 % Rotamer: Outliers : 3.29 % Allowed : 13.71 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.13), residues: 4412 helix: 2.53 (0.23), residues: 540 sheet: -0.68 (0.14), residues: 1300 loop : -1.39 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T 114 TYR 0.036 0.002 TYR K 357 PHE 0.037 0.002 PHE B 6 TRP 0.016 0.001 TRP B 235 HIS 0.014 0.001 HIS T 116 Details of bonding type rmsd covalent geometry : bond 0.00410 (35620) covalent geometry : angle 0.65315 (48488) SS BOND : bond 0.00399 ( 68) SS BOND : angle 1.52200 ( 136) hydrogen bonds : bond 0.03826 ( 991) hydrogen bonds : angle 5.28193 ( 2529) link_BETA1-4 : bond 0.00881 ( 24) link_BETA1-4 : angle 2.49241 ( 72) link_NAG-ASN : bond 0.00961 ( 12) link_NAG-ASN : angle 2.69608 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 644 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 VAL cc_start: 0.8764 (t) cc_final: 0.8555 (t) REVERT: C 8 MET cc_start: 0.4727 (mpp) cc_final: 0.4211 (mpp) REVERT: D 122 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7411 (tm-30) REVERT: D 123 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8086 (p) REVERT: D 183 LYS cc_start: 0.7519 (pptt) cc_final: 0.7103 (tppt) REVERT: D 229 ARG cc_start: 0.6986 (mtm110) cc_final: 0.5865 (ptm160) REVERT: F 338 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8322 (p) REVERT: G 31 MET cc_start: 0.6214 (mmt) cc_final: 0.5982 (mmp) REVERT: G 175 ASN cc_start: 0.6852 (t0) cc_final: 0.6579 (t0) REVERT: G 234 THR cc_start: 0.8333 (t) cc_final: 0.8109 (p) REVERT: G 287 PHE cc_start: 0.7568 (m-80) cc_final: 0.7143 (m-80) REVERT: G 296 ILE cc_start: 0.7803 (mm) cc_final: 0.7582 (mm) REVERT: H 209 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7231 (mt-10) REVERT: H 245 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7374 (mppt) REVERT: H 402 MET cc_start: 0.7208 (mmt) cc_final: 0.6845 (tpp) REVERT: I 169 MET cc_start: 0.5783 (OUTLIER) cc_final: 0.5515 (ttm) REVERT: I 215 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.4899 (tmm) REVERT: I 246 ASP cc_start: 0.7242 (p0) cc_final: 0.6795 (t0) REVERT: I 358 TYR cc_start: 0.7223 (m-80) cc_final: 0.6862 (m-80) REVERT: J 150 GLU cc_start: 0.6807 (mp0) cc_final: 0.6488 (mt-10) REVERT: J 180 LEU cc_start: 0.6189 (pt) cc_final: 0.4195 (pt) REVERT: K 22 CYS cc_start: 0.7937 (t) cc_final: 0.7607 (m) REVERT: K 256 ILE cc_start: 0.8727 (pt) cc_final: 0.8463 (pt) REVERT: K 269 MET cc_start: 0.7883 (mtm) cc_final: 0.7612 (mtm) REVERT: L 45 ARG cc_start: 0.7484 (tpp80) cc_final: 0.7163 (tpp80) REVERT: O 141 MET cc_start: 0.7114 (mpp) cc_final: 0.6594 (mmp) REVERT: Q 177 MET cc_start: 0.6559 (mtt) cc_final: 0.6273 (mpp) REVERT: R 110 MET cc_start: 0.2068 (ptp) cc_final: 0.0481 (ttm) REVERT: S 110 MET cc_start: 0.3587 (OUTLIER) cc_final: 0.2432 (ppp) outliers start: 124 outliers final: 78 residues processed: 718 average time/residue: 0.1690 time to fit residues: 208.3108 Evaluate side-chains 617 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 533 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 95 PHE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 291 VAL Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 169 MET Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 283 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain J residue 387 MET Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 387 MET Chi-restraints excluded: chain O residue 124 LYS Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 175 VAL Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 170 CYS Chi-restraints excluded: chain Q residue 215 LYS Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 248 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain S residue 110 MET Chi-restraints excluded: chain S residue 113 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 328 optimal weight: 1.9990 chunk 323 optimal weight: 5.9990 chunk 312 optimal weight: 9.9990 chunk 434 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 300 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS B 232 HIS F 43 ASN ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS H 18 HIS H 152 HIS I 131 HIS I 212 ASN K 62 HIS Q 196 HIS S 126 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.174686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128964 restraints weight = 47049.887| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.29 r_work: 0.3295 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 35724 Z= 0.174 Angle : 0.683 11.158 48732 Z= 0.348 Chirality : 0.047 0.410 5476 Planarity : 0.005 0.059 6244 Dihedral : 6.067 59.000 5548 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.21 % Favored : 93.59 % Rotamer: Outliers : 3.87 % Allowed : 15.85 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.13), residues: 4412 helix: 2.38 (0.23), residues: 540 sheet: -0.70 (0.14), residues: 1300 loop : -1.40 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 133 TYR 0.046 0.002 TYR I 357 PHE 0.031 0.002 PHE B 6 TRP 0.021 0.001 TRP J 235 HIS 0.011 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00412 (35620) covalent geometry : angle 0.66952 (48488) SS BOND : bond 0.00493 ( 68) SS BOND : angle 1.55217 ( 136) hydrogen bonds : bond 0.03261 ( 991) hydrogen bonds : angle 5.03758 ( 2529) link_BETA1-4 : bond 0.00660 ( 24) link_BETA1-4 : angle 2.53129 ( 72) link_NAG-ASN : bond 0.00692 ( 12) link_NAG-ASN : angle 2.26757 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 581 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 TYR cc_start: 0.7950 (t80) cc_final: 0.7216 (t80) REVERT: A 20 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7455 (mt-10) REVERT: A 381 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7675 (tp30) REVERT: A 434 ILE cc_start: 0.7746 (mt) cc_final: 0.7444 (mm) REVERT: B 8 VAL cc_start: 0.8472 (t) cc_final: 0.8200 (m) REVERT: B 16 ILE cc_start: 0.7776 (mt) cc_final: 0.7523 (mt) REVERT: B 157 GLN cc_start: 0.7511 (tt0) cc_final: 0.7289 (mm110) REVERT: B 215 MET cc_start: 0.5999 (mmm) cc_final: 0.5377 (tpt) REVERT: B 269 MET cc_start: 0.8365 (mpp) cc_final: 0.8087 (mtt) REVERT: B 373 MET cc_start: 0.6895 (mmt) cc_final: 0.6037 (mtt) REVERT: D 183 LYS cc_start: 0.7642 (pptt) cc_final: 0.7366 (mmtp) REVERT: D 193 TYR cc_start: 0.6866 (m-80) cc_final: 0.6542 (m-80) REVERT: D 229 ARG cc_start: 0.6891 (mtm110) cc_final: 0.6227 (ptm160) REVERT: F 31 MET cc_start: 0.8343 (mtm) cc_final: 0.7903 (mtm) REVERT: F 321 LYS cc_start: 0.8093 (mtmm) cc_final: 0.7812 (mtmm) REVERT: G 42 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7084 (mp) REVERT: G 87 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7426 (t80) REVERT: G 275 ASN cc_start: 0.8085 (m-40) cc_final: 0.7706 (m-40) REVERT: G 357 SER cc_start: 0.8718 (p) cc_final: 0.8492 (p) REVERT: G 384 LYS cc_start: 0.7837 (mmtm) cc_final: 0.7568 (mmtm) REVERT: H 50 GLU cc_start: 0.7168 (pm20) cc_final: 0.6929 (tt0) REVERT: H 115 ARG cc_start: 0.7842 (ptt-90) cc_final: 0.7341 (ptm160) REVERT: H 245 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8270 (mppt) REVERT: H 338 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.8821 (p) REVERT: H 381 GLU cc_start: 0.8496 (pm20) cc_final: 0.7408 (mm-30) REVERT: H 402 MET cc_start: 0.7642 (mmt) cc_final: 0.7222 (tpp) REVERT: I 215 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5690 (tmm) REVERT: I 246 ASP cc_start: 0.7410 (p0) cc_final: 0.6872 (t0) REVERT: J 97 MET cc_start: 0.8765 (tpp) cc_final: 0.8516 (tpt) REVERT: J 111 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7750 (tt) REVERT: J 132 ASP cc_start: 0.8551 (t70) cc_final: 0.8240 (t70) REVERT: J 180 LEU cc_start: 0.5545 (pt) cc_final: 0.5243 (pp) REVERT: J 236 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7522 (tp-100) REVERT: J 250 ARG cc_start: 0.7493 (mtp-110) cc_final: 0.7223 (ptm-80) REVERT: J 299 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8108 (pp) REVERT: J 392 ARG cc_start: 0.7017 (tmm-80) cc_final: 0.6589 (ttt-90) REVERT: Q 111 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.5900 (ttp) REVERT: Q 177 MET cc_start: 0.6624 (mtt) cc_final: 0.6323 (mpp) REVERT: Q 231 VAL cc_start: 0.8012 (t) cc_final: 0.7573 (m) REVERT: S 110 MET cc_start: 0.3949 (ppp) cc_final: 0.3412 (ppp) REVERT: S 132 TRP cc_start: 0.7987 (m-10) cc_final: 0.7753 (m-10) outliers start: 146 outliers final: 88 residues processed: 681 average time/residue: 0.2053 time to fit residues: 235.2701 Evaluate side-chains 590 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 494 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 333 ASP Chi-restraints excluded: chain K residue 387 MET Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 223 ILE Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 173 ILE Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain Q residue 170 CYS Chi-restraints excluded: chain Q residue 215 LYS Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain S residue 113 CYS Chi-restraints excluded: chain S residue 126 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 285 optimal weight: 0.9980 chunk 433 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS B 158 GLN B 232 HIS B 255 HIS D 252 ASN F 116 HIS F 325 ASN G 3 HIS G 340 GLN I 62 HIS I 356 GLN J 340 GLN K 62 HIS K 226 HIS K 348 HIS O 252 ASN P 197 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123793 restraints weight = 46685.957| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.51 r_work: 0.3201 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.8956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 35724 Z= 0.206 Angle : 0.712 13.595 48732 Z= 0.362 Chirality : 0.048 0.266 5476 Planarity : 0.005 0.061 6244 Dihedral : 6.075 59.020 5548 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.78 % Favored : 93.06 % Rotamer: Outliers : 4.37 % Allowed : 17.29 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.13), residues: 4412 helix: 2.46 (0.23), residues: 536 sheet: -0.68 (0.14), residues: 1316 loop : -1.49 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 178 TYR 0.027 0.002 TYR A 46 PHE 0.023 0.002 PHE B 237 TRP 0.016 0.001 TRP O 251 HIS 0.011 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00499 (35620) covalent geometry : angle 0.69549 (48488) SS BOND : bond 0.00417 ( 68) SS BOND : angle 2.19684 ( 136) hydrogen bonds : bond 0.03901 ( 991) hydrogen bonds : angle 5.13824 ( 2529) link_BETA1-4 : bond 0.00919 ( 24) link_BETA1-4 : angle 2.24045 ( 72) link_NAG-ASN : bond 0.00635 ( 12) link_NAG-ASN : angle 2.37808 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 509 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: A 1 TYR cc_start: 0.8468 (t80) cc_final: 0.7804 (t80) REVERT: A 269 MET cc_start: 0.8517 (mtp) cc_final: 0.8237 (mtm) REVERT: A 370 CYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7166 (m) REVERT: B 76 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8066 (mp0) REVERT: B 157 GLN cc_start: 0.8083 (tt0) cc_final: 0.7855 (mm110) REVERT: B 215 MET cc_start: 0.6900 (mmm) cc_final: 0.6609 (tpt) REVERT: B 261 ASP cc_start: 0.8642 (t0) cc_final: 0.8421 (m-30) REVERT: D 122 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7192 (tm-30) REVERT: D 183 LYS cc_start: 0.7919 (pptt) cc_final: 0.7510 (tppt) REVERT: F 174 ASP cc_start: 0.8178 (p0) cc_final: 0.7961 (p0) REVERT: F 351 LYS cc_start: 0.8572 (ptmt) cc_final: 0.8068 (mtpp) REVERT: G 87 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7754 (t80) REVERT: G 99 GLU cc_start: 0.8362 (pm20) cc_final: 0.8086 (pm20) REVERT: G 126 THR cc_start: 0.9093 (t) cc_final: 0.8788 (p) REVERT: G 145 ASP cc_start: 0.7555 (p0) cc_final: 0.7288 (p0) REVERT: G 209 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7250 (tp30) REVERT: G 275 ASN cc_start: 0.8815 (m-40) cc_final: 0.8606 (m-40) REVERT: G 287 PHE cc_start: 0.8563 (m-80) cc_final: 0.8132 (m-10) REVERT: G 297 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7959 (mp) REVERT: G 339 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8345 (mp) REVERT: G 396 ASN cc_start: 0.8873 (t0) cc_final: 0.8497 (m-40) REVERT: H 7 MET cc_start: 0.9166 (ttt) cc_final: 0.8891 (ptm) REVERT: H 115 ARG cc_start: 0.8315 (ptt-90) cc_final: 0.7904 (ptm160) REVERT: H 381 GLU cc_start: 0.8693 (pm20) cc_final: 0.7670 (mm-30) REVERT: I 227 VAL cc_start: 0.8281 (t) cc_final: 0.7961 (m) REVERT: I 253 LYS cc_start: 0.8179 (mttp) cc_final: 0.7975 (mttt) REVERT: J 53 GLN cc_start: 0.8211 (pt0) cc_final: 0.7996 (pt0) REVERT: J 97 MET cc_start: 0.8940 (tpp) cc_final: 0.8729 (tpt) REVERT: J 231 ASP cc_start: 0.7204 (t0) cc_final: 0.6939 (t0) REVERT: J 340 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: K 325 MET cc_start: 0.9080 (ppp) cc_final: 0.8814 (ppp) REVERT: P 170 CYS cc_start: 0.6908 (p) cc_final: 0.6552 (m) REVERT: Q 255 MET cc_start: 0.6545 (mmm) cc_final: 0.6289 (tpt) REVERT: S 110 MET cc_start: 0.3818 (OUTLIER) cc_final: 0.3419 (ppp) REVERT: S 144 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7068 (mp0) outliers start: 165 outliers final: 112 residues processed: 630 average time/residue: 0.2021 time to fit residues: 215.8187 Evaluate side-chains 568 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 449 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 368 SER Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 291 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 169 MET Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 256 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 387 MET Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain O residue 124 LYS Chi-restraints excluded: chain O residue 175 VAL Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 215 LYS Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 248 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain S residue 110 MET Chi-restraints excluded: chain S residue 113 CYS Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 301 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 385 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 chunk 415 optimal weight: 9.9990 chunk 422 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 358 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 232 HIS B 255 HIS F 325 ASN G 3 HIS H 275 ASN K 226 HIS K 348 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.123314 restraints weight = 46587.402| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.39 r_work: 0.3209 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.9141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 35724 Z= 0.106 Angle : 0.593 9.423 48732 Z= 0.296 Chirality : 0.043 0.242 5476 Planarity : 0.004 0.054 6244 Dihedral : 5.664 59.572 5548 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.73 % Favored : 94.11 % Rotamer: Outliers : 3.37 % Allowed : 19.25 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.13), residues: 4412 helix: 2.65 (0.23), residues: 536 sheet: -0.64 (0.14), residues: 1292 loop : -1.35 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 250 TYR 0.023 0.001 TYR N 49 PHE 0.016 0.001 PHE B 237 TRP 0.011 0.001 TRP G 243 HIS 0.007 0.001 HIS K 255 Details of bonding type rmsd covalent geometry : bond 0.00244 (35620) covalent geometry : angle 0.58128 (48488) SS BOND : bond 0.00183 ( 68) SS BOND : angle 1.30160 ( 136) hydrogen bonds : bond 0.03057 ( 991) hydrogen bonds : angle 4.84255 ( 2529) link_BETA1-4 : bond 0.00779 ( 24) link_BETA1-4 : angle 2.24456 ( 72) link_NAG-ASN : bond 0.00409 ( 12) link_NAG-ASN : angle 1.99100 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 478 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: A 1 TYR cc_start: 0.8441 (t80) cc_final: 0.7671 (t80) REVERT: A 269 MET cc_start: 0.8325 (mtp) cc_final: 0.8123 (mtm) REVERT: A 370 CYS cc_start: 0.7586 (OUTLIER) cc_final: 0.6978 (m) REVERT: B 76 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7721 (mp0) REVERT: B 157 GLN cc_start: 0.8045 (tt0) cc_final: 0.7789 (mm110) REVERT: B 215 MET cc_start: 0.7024 (mmm) cc_final: 0.6812 (tpt) REVERT: B 261 ASP cc_start: 0.8585 (t0) cc_final: 0.8328 (m-30) REVERT: C 8 MET cc_start: 0.6658 (mpp) cc_final: 0.5859 (mpp) REVERT: D 122 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7117 (tm-30) REVERT: D 183 LYS cc_start: 0.7981 (pptt) cc_final: 0.7606 (tppt) REVERT: D 255 MET cc_start: 0.7100 (mmm) cc_final: 0.6866 (tpp) REVERT: F 38 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8618 (tp) REVERT: F 351 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8109 (mtpp) REVERT: G 87 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7686 (t80) REVERT: G 99 GLU cc_start: 0.8503 (pm20) cc_final: 0.8186 (pm20) REVERT: G 126 THR cc_start: 0.9032 (t) cc_final: 0.8703 (p) REVERT: G 136 MET cc_start: 0.7315 (ttm) cc_final: 0.7020 (mtm) REVERT: G 145 ASP cc_start: 0.7711 (p0) cc_final: 0.7441 (p0) REVERT: G 209 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7318 (tp30) REVERT: G 276 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8290 (mt) REVERT: G 297 ILE cc_start: 0.8249 (pt) cc_final: 0.7981 (mp) REVERT: G 339 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8370 (mp) REVERT: G 396 ASN cc_start: 0.8891 (t0) cc_final: 0.8427 (m-40) REVERT: H 7 MET cc_start: 0.9143 (ttt) cc_final: 0.8911 (ptm) REVERT: H 35 GLU cc_start: 0.8459 (tt0) cc_final: 0.8133 (tt0) REVERT: H 115 ARG cc_start: 0.8315 (ptt-90) cc_final: 0.7872 (ptm160) REVERT: H 228 MET cc_start: 0.8640 (ttm) cc_final: 0.8370 (ttm) REVERT: H 280 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7676 (ptp) REVERT: H 381 GLU cc_start: 0.8623 (pm20) cc_final: 0.7641 (mm-30) REVERT: I 96 THR cc_start: 0.7451 (m) cc_final: 0.7136 (p) REVERT: I 227 VAL cc_start: 0.8203 (t) cc_final: 0.7863 (m) REVERT: J 50 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7162 (m-10) REVERT: J 97 MET cc_start: 0.8849 (tpp) cc_final: 0.8647 (tpt) REVERT: K 67 ILE cc_start: 0.8206 (pt) cc_final: 0.7669 (mt) REVERT: K 96 THR cc_start: 0.8765 (m) cc_final: 0.8141 (p) REVERT: K 325 MET cc_start: 0.9061 (ppp) cc_final: 0.8778 (ppp) REVERT: P 170 CYS cc_start: 0.6729 (p) cc_final: 0.6474 (m) REVERT: Q 111 MET cc_start: 0.5971 (pmm) cc_final: 0.4885 (ttm) REVERT: Q 255 MET cc_start: 0.6527 (mmm) cc_final: 0.6288 (tpt) REVERT: R 110 MET cc_start: 0.3443 (ptp) cc_final: 0.2142 (ttp) REVERT: S 110 MET cc_start: 0.4131 (OUTLIER) cc_final: 0.3479 (ppp) REVERT: S 132 TRP cc_start: 0.8219 (m-10) cc_final: 0.7966 (m-10) REVERT: S 144 GLU cc_start: 0.7641 (mp0) cc_final: 0.7217 (mp0) REVERT: T 139 ASP cc_start: 0.6908 (m-30) cc_final: 0.6430 (m-30) outliers start: 127 outliers final: 94 residues processed: 570 average time/residue: 0.2031 time to fit residues: 196.6090 Evaluate side-chains 550 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 448 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 325 ASN Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 368 SER Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 362 TYR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 220 CYS Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 387 MET Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 215 LYS Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain S residue 110 MET Chi-restraints excluded: chain S residue 113 CYS Chi-restraints excluded: chain T residue 110 MET Chi-restraints excluded: chain T residue 131 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 135 optimal weight: 9.9990 chunk 390 optimal weight: 10.0000 chunk 397 optimal weight: 40.0000 chunk 51 optimal weight: 8.9990 chunk 313 optimal weight: 10.0000 chunk 405 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 416 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 232 HIS D 252 ASN F 235 GLN F 325 ASN G 3 HIS G 30 GLN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 328 HIS O 145 HIS O 196 HIS O 252 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.159138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113961 restraints weight = 46508.719| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.50 r_work: 0.3038 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 1.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.108 35724 Z= 0.419 Angle : 0.940 14.273 48732 Z= 0.486 Chirality : 0.058 0.354 5476 Planarity : 0.007 0.078 6244 Dihedral : 7.099 58.435 5548 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.59 % Favored : 90.25 % Rotamer: Outliers : 5.43 % Allowed : 18.58 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.12), residues: 4412 helix: 1.84 (0.23), residues: 516 sheet: -1.31 (0.14), residues: 1296 loop : -1.89 (0.11), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 206 TYR 0.040 0.003 TYR N 49 PHE 0.043 0.003 PHE I 50 TRP 0.033 0.003 TRP K 235 HIS 0.015 0.003 HIS K 73 Details of bonding type rmsd covalent geometry : bond 0.01028 (35620) covalent geometry : angle 0.92567 (48488) SS BOND : bond 0.00703 ( 68) SS BOND : angle 2.27103 ( 136) hydrogen bonds : bond 0.05366 ( 991) hydrogen bonds : angle 5.76580 ( 2529) link_BETA1-4 : bond 0.01146 ( 24) link_BETA1-4 : angle 2.60125 ( 72) link_NAG-ASN : bond 0.00868 ( 12) link_NAG-ASN : angle 3.14783 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 441 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6725 (p90) REVERT: A 319 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8855 (p) REVERT: B 76 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7880 (mp0) REVERT: B 157 GLN cc_start: 0.8404 (tp40) cc_final: 0.7918 (mm110) REVERT: B 182 SER cc_start: 0.8039 (m) cc_final: 0.7762 (t) REVERT: B 215 MET cc_start: 0.7678 (mmm) cc_final: 0.7147 (tpt) REVERT: B 280 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7745 (mpp80) REVERT: B 373 MET cc_start: 0.7705 (mmt) cc_final: 0.6767 (mtm) REVERT: C 8 MET cc_start: 0.7267 (mpp) cc_final: 0.6705 (mpp) REVERT: C 53 GLN cc_start: 0.7774 (tt0) cc_final: 0.7156 (tp-100) REVERT: D 122 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7126 (tm-30) REVERT: D 183 LYS cc_start: 0.8422 (pttt) cc_final: 0.8002 (ttpt) REVERT: D 255 MET cc_start: 0.7196 (mmm) cc_final: 0.6979 (ttp) REVERT: F 1 TYR cc_start: 0.8679 (t80) cc_final: 0.8178 (t80) REVERT: F 182 ASP cc_start: 0.8771 (p0) cc_final: 0.8458 (p0) REVERT: F 242 TYR cc_start: 0.7024 (m-80) cc_final: 0.6600 (m-10) REVERT: F 351 LYS cc_start: 0.8848 (ptmt) cc_final: 0.8499 (mtpp) REVERT: G 31 MET cc_start: 0.8845 (mmt) cc_final: 0.8369 (mtt) REVERT: G 177 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8774 (tt) REVERT: G 209 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7501 (tp30) REVERT: G 241 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8368 (mtpp) REVERT: G 246 GLU cc_start: 0.6150 (pt0) cc_final: 0.5729 (pt0) REVERT: G 324 LYS cc_start: 0.6697 (ptpp) cc_final: 0.6438 (mmmm) REVERT: G 340 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8633 (tt0) REVERT: H 38 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8899 (mp) REVERT: H 87 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7554 (t80) REVERT: H 115 ARG cc_start: 0.8759 (ptt-90) cc_final: 0.8486 (ptm160) REVERT: H 117 ASP cc_start: 0.8597 (m-30) cc_final: 0.7935 (p0) REVERT: H 228 MET cc_start: 0.8989 (ttm) cc_final: 0.8677 (ttm) REVERT: H 244 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8871 (mp) REVERT: H 245 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8940 (mppt) REVERT: H 338 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9134 (p) REVERT: I 168 ASP cc_start: 0.8150 (m-30) cc_final: 0.7760 (m-30) REVERT: I 199 TYR cc_start: 0.5887 (p90) cc_final: 0.5395 (p90) REVERT: J 50 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8112 (m-10) REVERT: J 128 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8729 (tt0) REVERT: J 166 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8558 (mm-30) REVERT: J 178 ARG cc_start: 0.7925 (mmm-85) cc_final: 0.7720 (mmm-85) REVERT: K 232 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.6059 (m-70) REVERT: K 331 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.8872 (t0) REVERT: L 45 ARG cc_start: 0.8304 (tpp80) cc_final: 0.8049 (tpp80) REVERT: M 29 GLU cc_start: 0.7986 (mp0) cc_final: 0.7583 (mp0) REVERT: N 41 ASP cc_start: 0.8043 (m-30) cc_final: 0.7364 (m-30) REVERT: P 251 TRP cc_start: 0.8368 (m-10) cc_final: 0.7993 (m-10) REVERT: Q 215 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7206 (ttpp) REVERT: Q 255 MET cc_start: 0.6896 (mmm) cc_final: 0.6684 (tpt) REVERT: S 110 MET cc_start: 0.4424 (OUTLIER) cc_final: 0.3645 (ppp) REVERT: S 144 GLU cc_start: 0.7995 (mp0) cc_final: 0.7240 (mp0) REVERT: T 139 ASP cc_start: 0.7467 (m-30) cc_final: 0.6895 (m-30) outliers start: 205 outliers final: 147 residues processed: 603 average time/residue: 0.2050 time to fit residues: 209.1077 Evaluate side-chains 570 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 407 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 310 SER Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 340 GLN Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 368 SER Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 291 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 128 GLN Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 220 CYS Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain K residue 387 MET Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain O residue 124 LYS Chi-restraints excluded: chain O residue 175 VAL Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain P residue 113 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 215 LYS Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain S residue 110 MET Chi-restraints excluded: chain S residue 113 CYS Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain T residue 118 ILE Chi-restraints excluded: chain T residue 131 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 5 optimal weight: 0.6980 chunk 227 optimal weight: 0.1980 chunk 116 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 421 optimal weight: 20.0000 chunk 84 optimal weight: 0.0870 chunk 270 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 174 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN B 232 HIS D 201 GLN D 252 ASN F 235 GLN H 118 HIS I 62 HIS I 287 HIS J 53 GLN ** J 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN K 328 HIS O 252 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.167158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120967 restraints weight = 46346.489| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.60 r_work: 0.3159 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 1.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35724 Z= 0.115 Angle : 0.634 9.888 48732 Z= 0.321 Chirality : 0.044 0.251 5476 Planarity : 0.005 0.076 6244 Dihedral : 6.065 59.584 5548 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.94 % Favored : 93.95 % Rotamer: Outliers : 3.18 % Allowed : 21.42 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.12), residues: 4412 helix: 2.36 (0.23), residues: 536 sheet: -0.87 (0.15), residues: 1196 loop : -1.63 (0.11), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 119 TYR 0.028 0.001 TYR N 48 PHE 0.022 0.001 PHE L 19 TRP 0.018 0.001 TRP I 329 HIS 0.012 0.001 HIS I 255 Details of bonding type rmsd covalent geometry : bond 0.00257 (35620) covalent geometry : angle 0.62217 (48488) SS BOND : bond 0.00434 ( 68) SS BOND : angle 1.29409 ( 136) hydrogen bonds : bond 0.03436 ( 991) hydrogen bonds : angle 5.13016 ( 2529) link_BETA1-4 : bond 0.00866 ( 24) link_BETA1-4 : angle 2.30246 ( 72) link_NAG-ASN : bond 0.00479 ( 12) link_NAG-ASN : angle 2.35538 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 464 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7389 (tptt) cc_final: 0.7165 (tttp) REVERT: A 295 THR cc_start: 0.9133 (m) cc_final: 0.8900 (p) REVERT: B 119 ARG cc_start: 0.8851 (mpp80) cc_final: 0.8648 (mtm-85) REVERT: B 157 GLN cc_start: 0.8389 (tp40) cc_final: 0.8041 (mm110) REVERT: B 171 MET cc_start: 0.8936 (tpp) cc_final: 0.8712 (mmm) REVERT: B 182 SER cc_start: 0.7861 (m) cc_final: 0.7660 (t) REVERT: B 251 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8419 (mmtm) REVERT: B 373 MET cc_start: 0.7630 (mmt) cc_final: 0.6733 (mtm) REVERT: C 8 MET cc_start: 0.7190 (mpp) cc_final: 0.6669 (mpp) REVERT: C 53 GLN cc_start: 0.7773 (tt0) cc_final: 0.7106 (tp40) REVERT: D 122 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7029 (tm-30) REVERT: D 255 MET cc_start: 0.7097 (mmm) cc_final: 0.6808 (ttp) REVERT: F 182 ASP cc_start: 0.8745 (p0) cc_final: 0.8418 (p0) REVERT: F 351 LYS cc_start: 0.8827 (ptmt) cc_final: 0.8397 (mtpp) REVERT: G 31 MET cc_start: 0.8390 (mmt) cc_final: 0.7998 (mtt) REVERT: G 126 THR cc_start: 0.9243 (t) cc_final: 0.8976 (p) REVERT: G 209 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7592 (tp30) REVERT: G 324 LYS cc_start: 0.6808 (ptpp) cc_final: 0.6437 (mmmm) REVERT: H 115 ARG cc_start: 0.8685 (ptt-90) cc_final: 0.8441 (ptm160) REVERT: H 117 ASP cc_start: 0.8494 (m-30) cc_final: 0.7971 (p0) REVERT: H 228 MET cc_start: 0.8744 (ttm) cc_final: 0.8503 (ttm) REVERT: I 96 THR cc_start: 0.7507 (m) cc_final: 0.7220 (p) REVERT: I 199 TYR cc_start: 0.5712 (p90) cc_final: 0.5408 (p90) REVERT: J 50 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7466 (m-10) REVERT: J 178 ARG cc_start: 0.7843 (mmm-85) cc_final: 0.7598 (mmm-85) REVERT: J 236 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8649 (tm-30) REVERT: J 340 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: K 50 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7786 (m-10) REVERT: K 232 HIS cc_start: 0.6393 (OUTLIER) cc_final: 0.5787 (m-70) REVERT: L 45 ARG cc_start: 0.8271 (tpp80) cc_final: 0.7989 (tpp80) REVERT: M 29 GLU cc_start: 0.7916 (mp0) cc_final: 0.7608 (mp0) REVERT: N 41 ASP cc_start: 0.8056 (m-30) cc_final: 0.7566 (m-30) REVERT: P 141 MET cc_start: 0.7569 (mtp) cc_final: 0.7286 (mtp) REVERT: P 253 LYS cc_start: 0.7292 (pptt) cc_final: 0.6793 (mtpt) REVERT: Q 215 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7104 (ttpp) REVERT: S 110 MET cc_start: 0.4208 (OUTLIER) cc_final: 0.3477 (ppp) REVERT: T 139 ASP cc_start: 0.7164 (m-30) cc_final: 0.6593 (m-30) outliers start: 120 outliers final: 84 residues processed: 554 average time/residue: 0.2118 time to fit residues: 196.1333 Evaluate side-chains 522 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 431 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 362 TYR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 220 CYS Chi-restraints excluded: chain J residue 236 GLN Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain O residue 124 LYS Chi-restraints excluded: chain O residue 175 VAL Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 113 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 215 LYS Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain S residue 110 MET Chi-restraints excluded: chain S residue 113 CYS Chi-restraints excluded: chain T residue 110 MET Chi-restraints excluded: chain T residue 131 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 311 optimal weight: 9.9990 chunk 19 optimal weight: 0.0370 chunk 286 optimal weight: 0.0870 chunk 193 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 390 optimal weight: 30.0000 chunk 256 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 HIS D 201 GLN D 252 ASN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 ASN I 255 HIS J 238 ASN J 340 GLN K 212 ASN K 255 HIS M 42 ASN O 117 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.168725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122565 restraints weight = 46116.472| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.53 r_work: 0.3196 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 1.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 35724 Z= 0.108 Angle : 0.602 10.242 48732 Z= 0.303 Chirality : 0.044 0.288 5476 Planarity : 0.004 0.081 6244 Dihedral : 5.628 57.626 5548 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.26 % Favored : 93.63 % Rotamer: Outliers : 2.81 % Allowed : 22.08 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.13), residues: 4412 helix: 2.26 (0.23), residues: 560 sheet: -0.77 (0.14), residues: 1216 loop : -1.45 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 119 TYR 0.020 0.001 TYR P 184 PHE 0.036 0.001 PHE F 95 TRP 0.013 0.001 TRP J 338 HIS 0.013 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00247 (35620) covalent geometry : angle 0.59101 (48488) SS BOND : bond 0.00296 ( 68) SS BOND : angle 1.29831 ( 136) hydrogen bonds : bond 0.03042 ( 991) hydrogen bonds : angle 4.88878 ( 2529) link_BETA1-4 : bond 0.00782 ( 24) link_BETA1-4 : angle 2.18303 ( 72) link_NAG-ASN : bond 0.00346 ( 12) link_NAG-ASN : angle 2.04523 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 447 time to evaluate : 1.414 Fit side-chains REVERT: A 61 LYS cc_start: 0.7243 (tptt) cc_final: 0.7040 (tttp) REVERT: A 295 THR cc_start: 0.9075 (m) cc_final: 0.8856 (p) REVERT: B 76 GLU cc_start: 0.7989 (mp0) cc_final: 0.7642 (mp0) REVERT: B 157 GLN cc_start: 0.8269 (tp40) cc_final: 0.7974 (mm110) REVERT: B 373 MET cc_start: 0.7442 (mmt) cc_final: 0.6583 (mtm) REVERT: C 8 MET cc_start: 0.6897 (mpp) cc_final: 0.6438 (mpp) REVERT: C 53 GLN cc_start: 0.7789 (tt0) cc_final: 0.7163 (tp40) REVERT: D 122 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6755 (tm-30) REVERT: D 183 LYS cc_start: 0.8088 (pttt) cc_final: 0.7665 (ttmt) REVERT: D 255 MET cc_start: 0.7154 (mmm) cc_final: 0.6893 (ttp) REVERT: F 79 LYS cc_start: 0.8330 (ptmt) cc_final: 0.8004 (ptpp) REVERT: F 182 ASP cc_start: 0.8719 (p0) cc_final: 0.8268 (t0) REVERT: F 228 MET cc_start: 0.8106 (mtm) cc_final: 0.7867 (mtt) REVERT: F 302 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8148 (p) REVERT: F 351 LYS cc_start: 0.8818 (ptmt) cc_final: 0.8431 (mtpp) REVERT: F 384 LYS cc_start: 0.6502 (tttt) cc_final: 0.6295 (ttpt) REVERT: G 31 MET cc_start: 0.8333 (mmt) cc_final: 0.7853 (mtt) REVERT: G 126 THR cc_start: 0.9222 (t) cc_final: 0.8971 (p) REVERT: G 209 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7523 (tp30) REVERT: G 324 LYS cc_start: 0.6700 (ptpp) cc_final: 0.6331 (mmmm) REVERT: H 115 ARG cc_start: 0.8687 (ptt-90) cc_final: 0.8390 (ptm160) REVERT: H 117 ASP cc_start: 0.8422 (m-30) cc_final: 0.7956 (p0) REVERT: I 199 TYR cc_start: 0.5536 (p90) cc_final: 0.5204 (p90) REVERT: J 50 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7485 (m-10) REVERT: J 132 ASP cc_start: 0.8953 (t70) cc_final: 0.8512 (t0) REVERT: J 178 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7488 (mmm-85) REVERT: J 238 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8456 (t0) REVERT: J 340 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: K 50 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7772 (m-10) REVERT: K 53 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8326 (pt0) REVERT: K 232 HIS cc_start: 0.6376 (OUTLIER) cc_final: 0.5969 (m-70) REVERT: L 45 ARG cc_start: 0.8225 (tpp80) cc_final: 0.7930 (tpp80) REVERT: M 29 GLU cc_start: 0.7945 (mp0) cc_final: 0.7630 (mp0) REVERT: N 40 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7827 (mm-30) REVERT: N 41 ASP cc_start: 0.7977 (m-30) cc_final: 0.7407 (m-30) REVERT: Q 111 MET cc_start: 0.5858 (pmm) cc_final: 0.4958 (tmm) REVERT: Q 215 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7040 (ttpp) REVERT: E 133 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7928 (tpp80) REVERT: S 110 MET cc_start: 0.4313 (OUTLIER) cc_final: 0.3622 (ppp) REVERT: T 139 ASP cc_start: 0.6860 (m-30) cc_final: 0.6306 (m-30) outliers start: 106 outliers final: 82 residues processed: 527 average time/residue: 0.2102 time to fit residues: 185.6153 Evaluate side-chains 510 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 418 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 362 TYR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 220 CYS Chi-restraints excluded: chain J residue 238 ASN Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain J residue 340 GLN Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain O residue 124 LYS Chi-restraints excluded: chain O residue 175 VAL Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 113 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 215 LYS Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain S residue 110 MET Chi-restraints excluded: chain S residue 113 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 363 optimal weight: 0.0040 chunk 128 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 chunk 307 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 131 optimal weight: 0.3980 chunk 168 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 HIS ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN K 212 ASN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.169066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122838 restraints weight = 46386.203| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.51 r_work: 0.3199 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 1.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35724 Z= 0.106 Angle : 0.596 10.588 48732 Z= 0.300 Chirality : 0.044 0.234 5476 Planarity : 0.004 0.057 6244 Dihedral : 5.499 58.354 5548 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.05 % Favored : 93.83 % Rotamer: Outliers : 2.44 % Allowed : 22.43 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.13), residues: 4412 helix: 2.21 (0.23), residues: 568 sheet: -0.57 (0.14), residues: 1268 loop : -1.44 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 119 TYR 0.021 0.001 TYR N 48 PHE 0.029 0.001 PHE F 95 TRP 0.012 0.001 TRP J 235 HIS 0.009 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00248 (35620) covalent geometry : angle 0.58595 (48488) SS BOND : bond 0.00243 ( 68) SS BOND : angle 1.24483 ( 136) hydrogen bonds : bond 0.02921 ( 991) hydrogen bonds : angle 4.80410 ( 2529) link_BETA1-4 : bond 0.00732 ( 24) link_BETA1-4 : angle 2.16518 ( 72) link_NAG-ASN : bond 0.00335 ( 12) link_NAG-ASN : angle 1.97541 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8824 Ramachandran restraints generated. 4412 Oldfield, 0 Emsley, 4412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 429 time to evaluate : 1.098 Fit side-chains REVERT: A 61 LYS cc_start: 0.7161 (tptt) cc_final: 0.6929 (tttp) REVERT: A 295 THR cc_start: 0.9031 (m) cc_final: 0.8794 (p) REVERT: B 76 GLU cc_start: 0.8112 (mp0) cc_final: 0.7885 (mp0) REVERT: B 157 GLN cc_start: 0.8244 (tp40) cc_final: 0.7964 (mm110) REVERT: B 373 MET cc_start: 0.7378 (mmt) cc_final: 0.6531 (mtm) REVERT: B 387 MET cc_start: 0.7669 (ttp) cc_final: 0.7450 (ttp) REVERT: C 8 MET cc_start: 0.6888 (mpp) cc_final: 0.6461 (mpp) REVERT: C 53 GLN cc_start: 0.7796 (tt0) cc_final: 0.7164 (tp40) REVERT: D 122 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6745 (tm-30) REVERT: D 183 LYS cc_start: 0.8091 (pttt) cc_final: 0.7807 (ttpt) REVERT: D 255 MET cc_start: 0.7205 (mmm) cc_final: 0.6920 (ttp) REVERT: F 182 ASP cc_start: 0.8716 (p0) cc_final: 0.8291 (t0) REVERT: F 244 LEU cc_start: 0.8995 (tt) cc_final: 0.8777 (tp) REVERT: F 302 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8146 (p) REVERT: F 351 LYS cc_start: 0.8837 (ptmt) cc_final: 0.8437 (mtpp) REVERT: G 31 MET cc_start: 0.8361 (mmt) cc_final: 0.7859 (mtt) REVERT: G 126 THR cc_start: 0.9217 (t) cc_final: 0.8978 (p) REVERT: G 209 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7575 (tp30) REVERT: G 324 LYS cc_start: 0.6695 (ptpp) cc_final: 0.6308 (mmmm) REVERT: H 115 ARG cc_start: 0.8682 (ptt-90) cc_final: 0.8389 (ptm160) REVERT: H 117 ASP cc_start: 0.8418 (m-30) cc_final: 0.7966 (p0) REVERT: I 199 TYR cc_start: 0.5563 (p90) cc_final: 0.5217 (p90) REVERT: I 223 GLU cc_start: 0.8679 (pm20) cc_final: 0.8459 (pm20) REVERT: I 227 VAL cc_start: 0.8570 (t) cc_final: 0.8111 (m) REVERT: J 50 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7466 (m-10) REVERT: J 132 ASP cc_start: 0.8950 (t70) cc_final: 0.8507 (t0) REVERT: J 269 MET cc_start: 0.8536 (mmm) cc_final: 0.8091 (mtt) REVERT: K 50 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7725 (m-10) REVERT: K 53 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8400 (pt0) REVERT: K 232 HIS cc_start: 0.6495 (OUTLIER) cc_final: 0.6150 (m-70) REVERT: K 247 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7126 (tp30) REVERT: L 45 ARG cc_start: 0.8213 (tpp80) cc_final: 0.7919 (tpp80) REVERT: M 29 GLU cc_start: 0.8031 (mp0) cc_final: 0.7704 (mp0) REVERT: N 40 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: N 41 ASP cc_start: 0.7993 (m-30) cc_final: 0.7450 (m-30) REVERT: Q 221 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7897 (mtp85) REVERT: S 110 MET cc_start: 0.4342 (OUTLIER) cc_final: 0.3581 (ppp) REVERT: T 139 ASP cc_start: 0.6783 (m-30) cc_final: 0.6208 (m-30) outliers start: 92 outliers final: 77 residues processed: 500 average time/residue: 0.1914 time to fit residues: 160.9544 Evaluate side-chains 504 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 420 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 362 TYR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 220 CYS Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 310 VAL Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 175 VAL Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain P residue 113 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain S residue 110 MET Chi-restraints excluded: chain S residue 113 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 238 optimal weight: 7.9990 chunk 348 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 376 optimal weight: 40.0000 chunk 292 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 328 HIS O 252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115028 restraints weight = 45829.184| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.39 r_work: 0.3098 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 1.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 35724 Z= 0.229 Angle : 0.705 10.970 48732 Z= 0.357 Chirality : 0.048 0.226 5476 Planarity : 0.005 0.070 6244 Dihedral : 5.932 59.894 5548 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.68 % Favored : 92.18 % Rotamer: Outliers : 2.78 % Allowed : 22.24 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.13), residues: 4412 helix: 2.16 (0.23), residues: 560 sheet: -0.91 (0.14), residues: 1268 loop : -1.60 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 119 TYR 0.026 0.002 TYR N 49 PHE 0.036 0.002 PHE F 95 TRP 0.019 0.002 TRP P 251 HIS 0.010 0.002 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00573 (35620) covalent geometry : angle 0.69274 (48488) SS BOND : bond 0.00287 ( 68) SS BOND : angle 1.70369 ( 136) hydrogen bonds : bond 0.03819 ( 991) hydrogen bonds : angle 5.07139 ( 2529) link_BETA1-4 : bond 0.00784 ( 24) link_BETA1-4 : angle 2.19133 ( 72) link_NAG-ASN : bond 0.00429 ( 12) link_NAG-ASN : angle 2.38402 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11530.90 seconds wall clock time: 197 minutes 34.83 seconds (11854.83 seconds total)