Starting phenix.real_space_refine on Sun Jun 29 14:25:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvz_39617/06_2025/8yvz_39617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvz_39617/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yvz_39617/06_2025/8yvz_39617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvz_39617/06_2025/8yvz_39617.map" model { file = "/net/cci-nas-00/data/ceres_data/8yvz_39617/06_2025/8yvz_39617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvz_39617/06_2025/8yvz_39617.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 1.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.96, per 1000 atoms: 0.60 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: 8.76 Conformation dependent library (CDL) restraints added in 4.6 seconds 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: 4.59 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: 14.28 Time building geometry restraints manager: 10.51 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: 0.04 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: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.460 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 79.080 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.360 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: 0.020 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.640 ------------------------------------------------------------------------------- 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 : 6.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (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 TRP 0.011 0.001 TRP J 329 HIS 0.007 0.001 HIS D 176 PHE 0.025 0.001 PHE J 50 TYR 0.022 0.001 TYR B 305 ARG 0.009 0.000 ARG H 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 12) link_NAG-ASN : angle 2.47683 ( 36) link_BETA1-4 : bond 0.00851 ( 24) link_BETA1-4 : angle 2.67470 ( 72) hydrogen bonds : bond 0.22389 ( 991) hydrogen bonds : angle 8.06298 ( 2529) SS BOND : bond 0.00432 ( 68) SS BOND : angle 1.12527 ( 136) covalent geometry : bond 0.00372 (35620) covalent geometry : angle 0.62775 (48488) *********************** 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 : 3.727 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: 0.6047 (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: 0.7088 (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: 0.6343 (tpp) REVERT: I 246 ASP cc_start: 0.6882 (p0) cc_final: 0.6633 (t0) REVERT: J 127 ILE cc_start: 0.5201 (tt) cc_final: 0.4895 (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: 0.6770 (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: -0.0333 (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: 0.5311 (m-10) outliers start: 3 outliers final: 0 residues processed: 949 average time/residue: 0.4612 time to fit residues: 706.0527 Evaluate side-chains 584 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 0.6980 chunk 330 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 222 optimal weight: 0.9980 chunk 176 optimal weight: 0.0000 chunk 341 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 254 optimal weight: 0.0870 chunk 395 optimal weight: 20.0000 overall best weight: 0.4962 ------------------------------------------------------------------------------- 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 I 356 GLN J 232 HIS J 306 HIS J 340 GLN K 131 HIS K 226 HIS ** O 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 ASN Q 172 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.174702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129395 restraints weight = 46397.301| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.73 r_work: 0.3297 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 35724 Z= 0.129 Angle : 0.673 10.775 48732 Z= 0.332 Chirality : 0.046 0.227 5476 Planarity : 0.005 0.067 6244 Dihedral : 9.764 74.748 5548 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.85 % Favored : 93.97 % Rotamer: Outliers : 2.68 % Allowed : 9.65 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4412 helix: 2.36 (0.23), residues: 552 sheet: -0.72 (0.14), residues: 1268 loop : -1.31 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 329 HIS 0.010 0.001 HIS G 3 PHE 0.025 0.001 PHE K 110 TYR 0.035 0.001 TYR A 93 ARG 0.006 0.001 ARG H 115 Details of bonding type rmsd link_NAG-ASN : bond 0.01202 ( 12) link_NAG-ASN : angle 3.38621 ( 36) link_BETA1-4 : bond 0.00850 ( 24) link_BETA1-4 : angle 3.34489 ( 72) hydrogen bonds : bond 0.03793 ( 991) hydrogen bonds : angle 5.88054 ( 2529) SS BOND : bond 0.00586 ( 68) SS BOND : angle 1.19201 ( 136) covalent geometry : bond 0.00279 (35620) covalent geometry : angle 0.65303 (48488) *********************** 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 739 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 638 time to evaluate : 4.743 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: B 151 ILE cc_start: 0.6781 (mm) cc_final: 0.6530 (mm) REVERT: B 387 MET cc_start: 0.6510 (mtp) cc_final: 0.6043 (ttp) REVERT: C 8 MET cc_start: 0.4898 (mpp) cc_final: 0.4204 (mpp) REVERT: D 124 LYS cc_start: 0.8407 (pttt) cc_final: 0.8022 (mtmm) REVERT: D 129 VAL cc_start: 0.6744 (p) cc_final: 0.6519 (m) REVERT: D 230 VAL cc_start: 0.5602 (t) cc_final: 0.5233 (p) REVERT: D 243 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7551 (mmm-85) REVERT: F 228 MET cc_start: 0.5049 (mmt) cc_final: 0.4531 (mmt) REVERT: G 77 GLN cc_start: 0.6784 (mm-40) cc_final: 0.6476 (mm-40) REVERT: G 140 VAL cc_start: 0.5669 (OUTLIER) cc_final: 0.5399 (t) REVERT: G 303 VAL cc_start: 0.7918 (t) cc_final: 0.7529 (p) REVERT: H 245 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.6064 (mppt) REVERT: H 402 MET cc_start: 0.6694 (mmt) cc_final: 0.6362 (tpp) REVERT: I 182 SER cc_start: 0.6896 (m) cc_final: 0.6478 (p) REVERT: I 226 HIS cc_start: 0.5374 (m170) cc_final: 0.5063 (t-170) REVERT: I 246 ASP cc_start: 0.7146 (p0) cc_final: 0.6613 (t0) REVERT: J 97 MET cc_start: 0.6898 (mmm) cc_final: 0.6573 (tpt) REVERT: J 232 HIS cc_start: 0.5417 (p90) cc_final: 0.4936 (m170) REVERT: J 297 ARG cc_start: 0.5286 (ptt90) cc_final: 0.4984 (ptt180) REVERT: K 118 THR cc_start: 0.2397 (m) cc_final: 0.2081 (m) REVERT: K 210 THR cc_start: 0.8631 (t) cc_final: 0.8226 (p) REVERT: K 269 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.5459 (mtm) REVERT: O 141 MET cc_start: 0.6565 (mpp) cc_final: 0.5938 (mpp) REVERT: P 113 MET cc_start: 0.7398 (mmt) cc_final: 0.7181 (mmt) REVERT: P 233 ILE cc_start: 0.6524 (mp) cc_final: 0.6271 (mt) REVERT: P 243 ARG cc_start: 0.6143 (mtp180) cc_final: 0.5858 (tpt170) REVERT: R 110 MET cc_start: 0.2070 (ptp) cc_final: 0.0266 (ttm) REVERT: S 110 MET cc_start: 0.3579 (ppp) cc_final: 0.3140 (pmm) REVERT: T 132 TRP cc_start: 0.5423 (m-10) cc_final: 0.5107 (m-10) outliers start: 101 outliers final: 61 residues processed: 690 average time/residue: 0.5003 time to fit residues: 582.7359 Evaluate side-chains 618 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 554 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR 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 281 ASN 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 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 140 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 225 SER 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 H residue 42 LEU 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 I residue 32 VAL Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain J residue 46 LEU 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 J residue 341 LEU 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 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 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 170 CYS Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain S residue 113 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 156 optimal weight: 0.9980 chunk 254 optimal weight: 20.0000 chunk 294 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 424 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 175 ASN B 61 ASN B 304 GLN D 201 GLN F 43 ASN F 160 GLN F 175 ASN ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 HIS G 3 HIS G 116 HIS H 152 HIS H 394 HIS ** I 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 331 ASN I 356 GLN J 61 ASN J 146 HIS J 183 GLN J 255 HIS K 7 ASN K 99 HIS K 226 HIS ** K 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 328 HIS ** K 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 ASN P 194 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.179024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133806 restraints weight = 47875.793| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.22 r_work: 0.3375 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.7305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 35724 Z= 0.261 Angle : 0.914 22.965 48732 Z= 0.466 Chirality : 0.053 0.265 5476 Planarity : 0.007 0.076 6244 Dihedral : 7.257 57.319 5548 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.71 % Favored : 92.04 % Rotamer: Outliers : 4.88 % Allowed : 13.52 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.12), residues: 4412 helix: 1.74 (0.23), residues: 548 sheet: -0.90 (0.14), residues: 1244 loop : -1.70 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 170 HIS 0.014 0.002 HIS A 118 PHE 0.054 0.003 PHE A 87 TYR 0.105 0.003 TYR K 357 ARG 0.012 0.001 ARG E 133 Details of bonding type rmsd link_NAG-ASN : bond 0.01126 ( 12) link_NAG-ASN : angle 3.12832 ( 36) link_BETA1-4 : bond 0.01063 ( 24) link_BETA1-4 : angle 2.69351 ( 72) hydrogen bonds : bond 0.05064 ( 991) hydrogen bonds : angle 5.81091 ( 2529) SS BOND : bond 0.01015 ( 68) SS BOND : angle 1.77906 ( 136) covalent geometry : bond 0.00608 (35620) covalent geometry : angle 0.90200 (48488) *********************** 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 816 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 632 time to evaluate : 4.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 TYR cc_start: 0.7923 (t80) cc_final: 0.7261 (t80) REVERT: A 20 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7574 (mt-10) REVERT: A 209 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8136 (mm-30) REVERT: A 434 ILE cc_start: 0.7840 (mt) cc_final: 0.7539 (mm) REVERT: B 157 GLN cc_start: 0.7598 (tt0) cc_final: 0.7358 (mm110) REVERT: B 174 ASP cc_start: 0.7621 (p0) cc_final: 0.7248 (p0) REVERT: B 175 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8364 (p) REVERT: B 269 MET cc_start: 0.8355 (mpp) cc_final: 0.8030 (mtt) REVERT: B 373 MET cc_start: 0.7055 (mmt) cc_final: 0.6155 (mtt) REVERT: C 8 MET cc_start: 0.5603 (mpp) cc_final: 0.5234 (mpp) REVERT: D 183 LYS cc_start: 0.7676 (pptt) cc_final: 0.7048 (tppt) REVERT: D 185 THR cc_start: 0.8808 (t) cc_final: 0.8532 (t) REVERT: D 193 TYR cc_start: 0.6906 (m-80) cc_final: 0.6514 (m-80) REVERT: D 229 ARG cc_start: 0.6949 (mtm110) cc_final: 0.6384 (ptp-110) REVERT: F 31 MET cc_start: 0.8510 (mtm) cc_final: 0.8173 (mtm) REVERT: F 79 LYS cc_start: 0.7730 (ptmt) cc_final: 0.7405 (ptpp) REVERT: F 290 ILE cc_start: 0.8679 (tt) cc_final: 0.8415 (tp) REVERT: F 321 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7844 (mtpp) REVERT: F 345 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7773 (mtpt) REVERT: G 42 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7285 (mp) REVERT: G 46 TYR cc_start: 0.9187 (p90) cc_final: 0.8698 (p90) REVERT: G 275 ASN cc_start: 0.8257 (m-40) cc_final: 0.8012 (m-40) REVERT: G 297 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7501 (mp) REVERT: H 4 SER cc_start: 0.8758 (m) cc_final: 0.8450 (t) REVERT: H 50 GLU cc_start: 0.7111 (pm20) cc_final: 0.6559 (tt0) REVERT: H 80 VAL cc_start: 0.8127 (t) cc_final: 0.7902 (p) REVERT: H 87 PHE cc_start: 0.8235 (m-80) cc_final: 0.7983 (t80) REVERT: H 245 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8600 (mppt) REVERT: H 334 SER cc_start: 0.8809 (t) cc_final: 0.8606 (t) REVERT: H 335 ASN cc_start: 0.8016 (t0) cc_final: 0.7703 (t0) REVERT: H 338 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.8802 (p) REVERT: H 381 GLU cc_start: 0.8157 (pm20) cc_final: 0.7767 (mm-30) REVERT: H 402 MET cc_start: 0.7609 (mmt) cc_final: 0.7226 (tpp) REVERT: I 215 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5534 (tmm) REVERT: I 246 ASP cc_start: 0.7577 (p0) cc_final: 0.7010 (t0) REVERT: I 325 MET cc_start: 0.8484 (ppp) cc_final: 0.7980 (ptt) REVERT: J 32 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7896 (m) REVERT: J 132 ASP cc_start: 0.8266 (t70) cc_final: 0.7806 (t70) REVERT: J 392 ARG cc_start: 0.6879 (tmm-80) cc_final: 0.6549 (ttt-90) REVERT: K 9 TYR cc_start: 0.4892 (m-80) cc_final: 0.4676 (m-10) REVERT: K 111 LEU cc_start: 0.8356 (pp) cc_final: 0.8152 (tt) REVERT: P 113 MET cc_start: 0.7308 (mmt) cc_final: 0.7081 (mmt) REVERT: Q 121 PHE cc_start: 0.7377 (m-80) cc_final: 0.7132 (m-80) REVERT: S 110 MET cc_start: 0.3625 (OUTLIER) cc_final: 0.2852 (ppp) REVERT: S 132 TRP cc_start: 0.7726 (m-10) cc_final: 0.7429 (m-10) outliers start: 184 outliers final: 90 residues processed: 759 average time/residue: 0.4176 time to fit residues: 537.2201 Evaluate side-chains 607 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 509 time to evaluate : 4.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 36 THR 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 360 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 291 VAL 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 339 LEU 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 32 GLN Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 108 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 316 LEU Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain H residue 19 ILE 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 245 LYS Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 291 VAL Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 388 VAL Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 111 LEU 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 215 MET Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 281 GLU Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 333 ASP Chi-restraints excluded: chain K residue 387 MET Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain O residue 124 LYS 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 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 136 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 T residue 118 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 310 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 384 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 chunk 347 optimal weight: 1.9990 chunk 422 optimal weight: 10.0000 chunk 354 optimal weight: 0.8980 chunk 305 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 274 optimal weight: 0.0010 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 175 ASN B 26 HIS B 232 HIS F 43 ASN G 3 HIS H 116 HIS I 53 GLN J 53 GLN J 99 HIS J 340 GLN K 53 GLN ** K 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 ASN K 277 HIS K 348 HIS O 197 HIS O 252 ASN P 197 HIS Q 196 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.174761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128456 restraints weight = 47314.665| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.28 r_work: 0.3292 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.7788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35724 Z= 0.127 Angle : 0.628 13.157 48732 Z= 0.314 Chirality : 0.045 0.243 5476 Planarity : 0.005 0.052 6244 Dihedral : 6.298 59.863 5548 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.67 % Favored : 94.13 % Rotamer: Outliers : 3.29 % Allowed : 16.89 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.12), residues: 4412 helix: 2.24 (0.23), residues: 548 sheet: -0.70 (0.14), residues: 1336 loop : -1.55 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 251 HIS 0.012 0.001 HIS I 226 PHE 0.018 0.001 PHE A 87 TYR 0.020 0.001 TYR L 49 ARG 0.008 0.000 ARG I 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 12) link_NAG-ASN : angle 2.18449 ( 36) link_BETA1-4 : bond 0.00796 ( 24) link_BETA1-4 : angle 2.47608 ( 72) hydrogen bonds : bond 0.03326 ( 991) hydrogen bonds : angle 5.21531 ( 2529) SS BOND : bond 0.00779 ( 68) SS BOND : angle 1.20024 ( 136) covalent geometry : bond 0.00287 (35620) covalent geometry : angle 0.61591 (48488) *********************** 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 655 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 531 time to evaluate : 3.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 TYR cc_start: 0.8119 (t80) cc_final: 0.7303 (t80) REVERT: A 20 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 136 MET cc_start: 0.8118 (mtp) cc_final: 0.7906 (mtp) REVERT: A 209 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8488 (mm-30) REVERT: A 381 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7663 (tp30) REVERT: A 434 ILE cc_start: 0.7778 (mt) cc_final: 0.7489 (mm) REVERT: B 16 ILE cc_start: 0.8007 (mt) cc_final: 0.7663 (mt) REVERT: B 158 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7779 (mp10) REVERT: B 251 LYS cc_start: 0.7367 (mtpp) cc_final: 0.6791 (mmtt) REVERT: B 373 MET cc_start: 0.7186 (mmt) cc_final: 0.6252 (mtt) REVERT: C 8 MET cc_start: 0.6198 (mpp) cc_final: 0.5964 (mpp) REVERT: D 141 MET cc_start: 0.7292 (mtp) cc_final: 0.7082 (mtp) REVERT: D 162 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6700 (tptp) REVERT: D 183 LYS cc_start: 0.7603 (pptt) cc_final: 0.7116 (tppt) REVERT: D 185 THR cc_start: 0.8790 (t) cc_final: 0.8557 (t) REVERT: D 229 ARG cc_start: 0.6940 (mtm110) cc_final: 0.6364 (ptm160) REVERT: F 4 SER cc_start: 0.9157 (t) cc_final: 0.8832 (m) REVERT: F 31 MET cc_start: 0.8555 (mtm) cc_final: 0.8126 (mtm) REVERT: F 88 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7801 (mtp) REVERT: F 290 ILE cc_start: 0.8767 (tt) cc_final: 0.8490 (tp) REVERT: G 31 MET cc_start: 0.7478 (mmt) cc_final: 0.6910 (mmp) REVERT: G 87 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7664 (t80) REVERT: G 287 PHE cc_start: 0.8161 (m-80) cc_final: 0.7895 (m-10) REVERT: G 297 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7817 (mp) REVERT: G 339 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7909 (mp) REVERT: H 50 GLU cc_start: 0.7594 (pm20) cc_final: 0.7261 (tt0) REVERT: H 87 PHE cc_start: 0.8353 (m-80) cc_final: 0.8068 (t80) REVERT: H 209 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7617 (mt-10) REVERT: H 245 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8512 (mppt) REVERT: H 335 ASN cc_start: 0.8049 (t0) cc_final: 0.7750 (t0) REVERT: H 338 THR cc_start: 0.9465 (t) cc_final: 0.8919 (p) REVERT: I 215 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.5819 (tmm) REVERT: I 325 MET cc_start: 0.8348 (ppp) cc_final: 0.7685 (ptt) REVERT: I 356 GLN cc_start: 0.8195 (tt0) cc_final: 0.7973 (tt0) REVERT: J 132 ASP cc_start: 0.8565 (t70) cc_final: 0.8177 (t70) REVERT: J 250 ARG cc_start: 0.7417 (ptm160) cc_final: 0.7030 (ptm-80) REVERT: K 178 ARG cc_start: 0.7737 (tpp80) cc_final: 0.7432 (tpm170) REVERT: K 325 MET cc_start: 0.8884 (ppp) cc_final: 0.8578 (ppp) REVERT: M 50 ASP cc_start: 0.7943 (t0) cc_final: 0.7504 (t70) REVERT: P 113 MET cc_start: 0.7396 (mmt) cc_final: 0.7187 (mmt) REVERT: Q 111 MET cc_start: 0.5148 (tpt) cc_final: 0.4492 (ptp) REVERT: Q 141 MET cc_start: 0.7242 (mpp) cc_final: 0.6832 (mpp) REVERT: E 126 GLN cc_start: 0.7375 (tt0) cc_final: 0.7070 (tt0) REVERT: S 110 MET cc_start: 0.3872 (ppp) cc_final: 0.3400 (ppp) REVERT: S 132 TRP cc_start: 0.7891 (m-10) cc_final: 0.7614 (m-10) outliers start: 124 outliers final: 83 residues processed: 611 average time/residue: 0.4318 time to fit residues: 447.9381 Evaluate side-chains 564 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 473 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 162 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 177 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 297 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 368 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 362 TYR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 174 ASP 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 305 TYR Chi-restraints excluded: chain K residue 333 ASP Chi-restraints excluded: chain K residue 362 TYR 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 182 SER Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 170 CYS 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 140 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 295 optimal weight: 40.0000 chunk 182 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 330 optimal weight: 4.9990 chunk 359 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 26 optimal weight: 0.0060 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 HIS ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 235 GLN G 3 HIS I 62 HIS I 290 HIS I 356 GLN J 255 HIS ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 348 HIS O 252 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.168910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122313 restraints weight = 46875.011| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.46 r_work: 0.3208 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.8679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35724 Z= 0.143 Angle : 0.615 9.473 48732 Z= 0.310 Chirality : 0.045 0.236 5476 Planarity : 0.005 0.054 6244 Dihedral : 5.810 58.164 5548 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.57 % Favored : 93.22 % Rotamer: Outliers : 3.92 % Allowed : 17.07 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4412 helix: 2.48 (0.23), residues: 544 sheet: -0.64 (0.14), residues: 1276 loop : -1.53 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 251 HIS 0.012 0.001 HIS B 255 PHE 0.024 0.001 PHE A 161 TYR 0.032 0.001 TYR B 305 ARG 0.005 0.000 ARG F 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 12) link_NAG-ASN : angle 2.05588 ( 36) link_BETA1-4 : bond 0.00829 ( 24) link_BETA1-4 : angle 2.24946 ( 72) hydrogen bonds : bond 0.03281 ( 991) hydrogen bonds : angle 4.99458 ( 2529) SS BOND : bond 0.00214 ( 68) SS BOND : angle 1.28666 ( 136) covalent geometry : bond 0.00338 (35620) covalent geometry : angle 0.60386 (48488) *********************** 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 660 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 512 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 MET cc_start: 0.8453 (mtp) cc_final: 0.8097 (mtm) REVERT: B 158 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: B 175 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8310 (p) REVERT: B 234 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8171 (mttm) REVERT: D 122 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8049 (tm-30) REVERT: D 162 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6815 (tptm) REVERT: D 183 LYS cc_start: 0.7901 (pptt) cc_final: 0.7256 (tppt) REVERT: D 185 THR cc_start: 0.8919 (t) cc_final: 0.8658 (t) REVERT: D 229 ARG cc_start: 0.7022 (mtm110) cc_final: 0.6003 (ptm160) REVERT: F 79 LYS cc_start: 0.8314 (ptmt) cc_final: 0.8030 (ptpp) REVERT: F 88 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8303 (mtp) REVERT: G 87 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7658 (t80) REVERT: G 99 GLU cc_start: 0.8439 (pm20) cc_final: 0.8173 (pm20) REVERT: G 126 THR cc_start: 0.8948 (t) cc_final: 0.8533 (p) REVERT: G 133 VAL cc_start: 0.8635 (m) cc_final: 0.8384 (m) REVERT: G 145 ASP cc_start: 0.7485 (p0) cc_final: 0.7232 (p0) REVERT: G 297 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8185 (mp) REVERT: G 339 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8213 (mp) REVERT: G 396 ASN cc_start: 0.8877 (t0) cc_final: 0.8491 (m-40) REVERT: H 50 GLU cc_start: 0.8030 (pm20) cc_final: 0.7804 (tt0) REVERT: H 88 MET cc_start: 0.8778 (ttm) cc_final: 0.8528 (mtt) REVERT: H 117 ASP cc_start: 0.8321 (m-30) cc_final: 0.7567 (p0) REVERT: H 209 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7662 (mt-10) REVERT: H 245 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8745 (mppt) REVERT: H 338 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.8923 (p) REVERT: I 166 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6583 (mm-30) REVERT: I 284 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8613 (mp) REVERT: J 231 ASP cc_start: 0.7009 (t0) cc_final: 0.6726 (t0) REVERT: J 250 ARG cc_start: 0.7739 (ptm160) cc_final: 0.7400 (ptm-80) REVERT: K 237 PHE cc_start: 0.8426 (t80) cc_final: 0.8196 (t80) REVERT: K 251 LYS cc_start: 0.7800 (ttpp) cc_final: 0.7416 (ttpp) REVERT: K 325 MET cc_start: 0.9078 (ppp) cc_final: 0.8769 (ppp) REVERT: M 50 ASP cc_start: 0.8168 (t0) cc_final: 0.7684 (t70) REVERT: M 53 GLN cc_start: 0.7358 (tp40) cc_final: 0.7031 (tp40) REVERT: P 113 MET cc_start: 0.7468 (mmt) cc_final: 0.7246 (mmt) REVERT: P 255 MET cc_start: 0.5729 (mmp) cc_final: 0.5457 (mmt) REVERT: Q 111 MET cc_start: 0.4948 (tpt) cc_final: 0.4397 (ptt) REVERT: Q 141 MET cc_start: 0.7453 (mpp) cc_final: 0.7189 (mpp) REVERT: Q 255 MET cc_start: 0.6455 (mmm) cc_final: 0.6241 (tpt) REVERT: S 110 MET cc_start: 0.3865 (OUTLIER) cc_final: 0.3247 (ppp) REVERT: S 132 TRP cc_start: 0.8171 (m-10) cc_final: 0.7921 (m-10) REVERT: T 117 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7553 (mt-10) REVERT: T 131 SER cc_start: 0.9138 (m) cc_final: 0.8932 (p) outliers start: 148 outliers final: 100 residues processed: 616 average time/residue: 0.4232 time to fit residues: 443.9564 Evaluate side-chains 573 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 462 time to evaluate : 3.519 ------------------------------------------------------------------------------- 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 60 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 279 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 VAL 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 154 THR Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 162 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 213 LEU 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 297 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 339 LEU Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 368 SER Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 366 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 139 GLU Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 111 LEU Chi-restraints excluded: chain K residue 163 THR 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 305 TYR Chi-restraints excluded: chain K residue 362 TYR 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 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain P residue 140 VAL 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 P residue 253 LYS Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 140 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 249 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain S residue 110 MET 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 431 optimal weight: 10.0000 chunk 399 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 170 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 360 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 232 HIS ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN H 264 ASN H 275 ASN I 62 HIS ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 ASN K 328 HIS O 252 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.166411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119733 restraints weight = 46398.323| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.46 r_work: 0.3165 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.9778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 35724 Z= 0.218 Angle : 0.684 10.084 48732 Z= 0.349 Chirality : 0.047 0.239 5476 Planarity : 0.005 0.055 6244 Dihedral : 6.057 59.116 5548 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.07 % Favored : 92.77 % Rotamer: Outliers : 4.93 % Allowed : 17.79 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4412 helix: 2.28 (0.23), residues: 544 sheet: -0.87 (0.13), residues: 1356 loop : -1.59 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 267 HIS 0.047 0.002 HIS I 290 PHE 0.021 0.002 PHE G 95 TYR 0.022 0.002 TYR K 69 ARG 0.013 0.001 ARG E 133 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 12) link_NAG-ASN : angle 2.32483 ( 36) link_BETA1-4 : bond 0.00861 ( 24) link_BETA1-4 : angle 2.34757 ( 72) hydrogen bonds : bond 0.03820 ( 991) hydrogen bonds : angle 5.14165 ( 2529) SS BOND : bond 0.00478 ( 68) SS BOND : angle 1.42565 ( 136) covalent geometry : bond 0.00535 (35620) covalent geometry : angle 0.67297 (48488) *********************** 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 660 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 474 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7984 (mp0) REVERT: B 171 MET cc_start: 0.8882 (tpp) cc_final: 0.8660 (tpt) REVERT: B 213 SER cc_start: 0.8179 (t) cc_final: 0.7924 (m) REVERT: D 122 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7672 (tm-30) REVERT: D 123 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8177 (p) REVERT: D 162 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7242 (tptm) REVERT: D 183 LYS cc_start: 0.8092 (pptt) cc_final: 0.7732 (ttpt) REVERT: F 79 LYS cc_start: 0.8464 (ptmt) cc_final: 0.8189 (ptpp) REVERT: F 351 LYS cc_start: 0.8641 (ptmt) cc_final: 0.8237 (mtpp) REVERT: G 31 MET cc_start: 0.8426 (mmt) cc_final: 0.7718 (mtt) REVERT: G 42 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7960 (mp) REVERT: G 126 THR cc_start: 0.9199 (t) cc_final: 0.8929 (p) REVERT: G 145 ASP cc_start: 0.8009 (p0) cc_final: 0.7794 (p0) REVERT: G 209 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7468 (tp30) REVERT: G 339 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8598 (mp) REVERT: H 88 MET cc_start: 0.8882 (ttm) cc_final: 0.8613 (mtt) REVERT: H 115 ARG cc_start: 0.8507 (ptt-90) cc_final: 0.8138 (ptm160) REVERT: H 117 ASP cc_start: 0.8417 (m-30) cc_final: 0.7730 (p0) REVERT: H 244 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8653 (mp) REVERT: H 338 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9061 (p) REVERT: H 364 SER cc_start: 0.9023 (t) cc_final: 0.8484 (m) REVERT: I 199 TYR cc_start: 0.5373 (p90) cc_final: 0.4850 (p90) REVERT: I 325 MET cc_start: 0.8888 (ppp) cc_final: 0.8334 (ptt) REVERT: I 373 MET cc_start: 0.8130 (mtt) cc_final: 0.7921 (mtm) REVERT: J 158 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: J 250 ARG cc_start: 0.8087 (ptm160) cc_final: 0.7759 (ptm-80) REVERT: K 35 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: K 251 LYS cc_start: 0.8004 (ttpp) cc_final: 0.7784 (mtpp) REVERT: L 45 ARG cc_start: 0.8008 (tpp80) cc_final: 0.7759 (tpp80) REVERT: M 53 GLN cc_start: 0.7552 (tp40) cc_final: 0.7139 (tp40) REVERT: N 41 ASP cc_start: 0.7983 (m-30) cc_final: 0.7536 (m-30) REVERT: P 113 MET cc_start: 0.7354 (mmt) cc_final: 0.6964 (mmp) REVERT: P 253 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6499 (mtpt) REVERT: Q 111 MET cc_start: 0.5194 (tpt) cc_final: 0.4609 (ptt) REVERT: Q 141 MET cc_start: 0.7657 (mpp) cc_final: 0.7379 (mpp) REVERT: Q 255 MET cc_start: 0.6734 (mmm) cc_final: 0.6475 (tpt) REVERT: S 110 MET cc_start: 0.4304 (OUTLIER) cc_final: 0.3670 (ppp) REVERT: S 132 TRP cc_start: 0.8569 (m-10) cc_final: 0.8317 (m-10) REVERT: T 117 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7738 (mt-10) REVERT: T 139 ASP cc_start: 0.7410 (m-30) cc_final: 0.6951 (m-30) REVERT: T 144 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8033 (mp0) outliers start: 186 outliers final: 130 residues processed: 612 average time/residue: 0.4154 time to fit residues: 428.5857 Evaluate side-chains 587 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 447 time to evaluate : 3.533 ------------------------------------------------------------------------------- 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 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 280 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 330 VAL 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 85 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 210 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 D residue 162 LYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 280 MET 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 329 SER Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain F residue 434 ILE 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 42 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 177 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 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 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 430 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 155 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 264 ASN Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 366 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 139 GLU 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 222 ILE Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 362 TYR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 220 CYS Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 220 CYS 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 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 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 264 SER Chi-restraints excluded: chain P residue 134 CYS Chi-restraints excluded: chain P residue 140 VAL 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 P residue 253 LYS Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 146 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 195 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 420 optimal weight: 0.0670 chunk 427 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 281 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 219 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 381 optimal weight: 30.0000 overall best weight: 1.8524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN B 226 HIS B 232 HIS D 125 HIS D 201 GLN F 235 GLN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 ASN T 116 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122016 restraints weight = 46459.904| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.53 r_work: 0.3178 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 1.0056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35724 Z= 0.133 Angle : 0.610 9.581 48732 Z= 0.306 Chirality : 0.045 0.237 5476 Planarity : 0.004 0.057 6244 Dihedral : 5.760 59.691 5548 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.19 % Favored : 93.65 % Rotamer: Outliers : 4.11 % Allowed : 19.25 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 4412 helix: 2.50 (0.23), residues: 544 sheet: -0.82 (0.14), residues: 1368 loop : -1.52 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 235 HIS 0.008 0.001 HIS I 226 PHE 0.018 0.001 PHE G 95 TYR 0.029 0.001 TYR N 49 ARG 0.007 0.000 ARG I 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 12) link_NAG-ASN : angle 2.09682 ( 36) link_BETA1-4 : bond 0.00720 ( 24) link_BETA1-4 : angle 2.22080 ( 72) hydrogen bonds : bond 0.03262 ( 991) hydrogen bonds : angle 4.96711 ( 2529) SS BOND : bond 0.00310 ( 68) SS BOND : angle 1.27917 ( 136) covalent geometry : bond 0.00320 (35620) covalent geometry : angle 0.59944 (48488) *********************** 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 626 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 471 time to evaluate : 3.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 171 MET cc_start: 0.8840 (tpp) cc_final: 0.8630 (tpt) REVERT: B 213 SER cc_start: 0.8221 (t) cc_final: 0.7966 (m) REVERT: B 373 MET cc_start: 0.7438 (mmt) cc_final: 0.6368 (mtm) REVERT: B 387 MET cc_start: 0.7537 (ttm) cc_final: 0.7258 (ttp) REVERT: D 122 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7457 (tm-30) REVERT: D 162 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7248 (tptm) REVERT: D 183 LYS cc_start: 0.8077 (pttt) cc_final: 0.7719 (tmmt) REVERT: F 79 LYS cc_start: 0.8467 (ptmt) cc_final: 0.8175 (ptpp) REVERT: F 351 LYS cc_start: 0.8675 (ptmt) cc_final: 0.8310 (mtpp) REVERT: G 31 MET cc_start: 0.8274 (mmt) cc_final: 0.7771 (mtt) REVERT: G 42 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7846 (mp) REVERT: G 68 CYS cc_start: 0.7920 (t) cc_final: 0.7520 (m) REVERT: G 87 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7563 (t80) REVERT: G 126 THR cc_start: 0.9251 (t) cc_final: 0.8991 (p) REVERT: G 145 ASP cc_start: 0.8102 (p0) cc_final: 0.7838 (p0) REVERT: G 209 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7533 (tp30) REVERT: G 339 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8686 (mp) REVERT: H 7 MET cc_start: 0.9210 (ttt) cc_final: 0.8999 (ptm) REVERT: H 88 MET cc_start: 0.8778 (ttm) cc_final: 0.8504 (mtt) REVERT: H 115 ARG cc_start: 0.8531 (ptt-90) cc_final: 0.8176 (ptm160) REVERT: H 117 ASP cc_start: 0.8410 (m-30) cc_final: 0.7824 (p0) REVERT: H 364 SER cc_start: 0.8968 (t) cc_final: 0.8464 (m) REVERT: I 96 THR cc_start: 0.7383 (m) cc_final: 0.7148 (p) REVERT: I 112 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: I 199 TYR cc_start: 0.5364 (p90) cc_final: 0.4989 (p90) REVERT: I 325 MET cc_start: 0.8714 (ppp) cc_final: 0.8057 (ptt) REVERT: I 373 MET cc_start: 0.8096 (mtt) cc_final: 0.7846 (mtm) REVERT: J 50 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: J 196 LYS cc_start: 0.7968 (mttt) cc_final: 0.7557 (mtmt) REVERT: J 250 ARG cc_start: 0.8087 (ptm160) cc_final: 0.7757 (ptm-80) REVERT: K 35 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: K 237 PHE cc_start: 0.8267 (t80) cc_final: 0.7899 (t80) REVERT: K 251 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7716 (mtpp) REVERT: L 45 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7778 (tpp80) REVERT: M 53 GLN cc_start: 0.7602 (tp40) cc_final: 0.7144 (tp40) REVERT: N 41 ASP cc_start: 0.7964 (m-30) cc_final: 0.7526 (m-30) REVERT: P 113 MET cc_start: 0.7343 (mmt) cc_final: 0.6906 (mmp) REVERT: P 253 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6604 (mtpt) REVERT: Q 111 MET cc_start: 0.5302 (tpt) cc_final: 0.4719 (ptt) REVERT: Q 255 MET cc_start: 0.6654 (mmm) cc_final: 0.6409 (tpt) REVERT: S 110 MET cc_start: 0.4266 (OUTLIER) cc_final: 0.3837 (ppp) REVERT: S 132 TRP cc_start: 0.8564 (m-10) cc_final: 0.8338 (m-10) REVERT: T 139 ASP cc_start: 0.7413 (m-30) cc_final: 0.6969 (m-30) REVERT: T 144 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8166 (mp0) outliers start: 155 outliers final: 110 residues processed: 590 average time/residue: 0.4288 time to fit residues: 428.2341 Evaluate side-chains 564 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 445 time to evaluate : 3.747 ------------------------------------------------------------------------------- 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 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 280 MET Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 319 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 53 GLN Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 162 LYS 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 68 CYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 279 SER 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 329 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 87 PHE 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 271 CYS Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 316 LEU 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 271 CYS Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 301 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 40 GLU Chi-restraints excluded: chain I residue 45 MET 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 139 GLU Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 299 LEU 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 I residue 411 LEU Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 220 CYS Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 220 CYS 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 305 TYR Chi-restraints excluded: chain K residue 392 ARG 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 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain P residue 140 VAL 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 P residue 253 LYS Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 146 VAL 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 131 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 184 optimal weight: 2.9990 chunk 396 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 354 optimal weight: 5.9990 chunk 373 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 167 optimal weight: 6.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 HIS B 232 HIS D 201 GLN D 252 ASN H 264 ASN H 275 ASN J 53 GLN J 238 ASN K 77 ASN K 212 ASN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.166292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120139 restraints weight = 45892.847| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.55 r_work: 0.3154 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 1.0338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35724 Z= 0.150 Angle : 0.620 9.496 48732 Z= 0.312 Chirality : 0.045 0.231 5476 Planarity : 0.004 0.053 6244 Dihedral : 5.701 58.744 5548 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.69 % Favored : 93.18 % Rotamer: Outliers : 4.14 % Allowed : 19.72 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.13), residues: 4412 helix: 2.53 (0.23), residues: 544 sheet: -0.77 (0.14), residues: 1352 loop : -1.54 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 235 HIS 0.007 0.001 HIS K 255 PHE 0.039 0.001 PHE L 19 TYR 0.023 0.001 TYR B 305 ARG 0.007 0.000 ARG B 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 12) link_NAG-ASN : angle 2.13992 ( 36) link_BETA1-4 : bond 0.00849 ( 24) link_BETA1-4 : angle 2.19436 ( 72) hydrogen bonds : bond 0.03325 ( 991) hydrogen bonds : angle 4.97502 ( 2529) SS BOND : bond 0.00266 ( 68) SS BOND : angle 1.29327 ( 136) covalent geometry : bond 0.00367 (35620) covalent geometry : angle 0.60889 (48488) *********************** 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 606 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 450 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7347 (tptt) cc_final: 0.7082 (tttp) REVERT: A 88 MET cc_start: 0.8221 (ptp) cc_final: 0.7866 (ptm) REVERT: A 319 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8852 (p) REVERT: B 76 GLU cc_start: 0.8047 (mp0) cc_final: 0.7832 (mp0) REVERT: B 119 ARG cc_start: 0.8773 (mpp80) cc_final: 0.8446 (mtm-85) REVERT: B 171 MET cc_start: 0.8876 (tpp) cc_final: 0.8655 (tpt) REVERT: B 213 SER cc_start: 0.8285 (t) cc_final: 0.8069 (m) REVERT: B 373 MET cc_start: 0.7443 (mmt) cc_final: 0.6458 (mtm) REVERT: C 53 GLN cc_start: 0.7754 (tt0) cc_final: 0.7043 (tp-100) REVERT: D 122 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7626 (tm-30) REVERT: F 79 LYS cc_start: 0.8422 (ptmt) cc_final: 0.8087 (ptpp) REVERT: F 182 ASP cc_start: 0.8686 (p0) cc_final: 0.8413 (p0) REVERT: F 351 LYS cc_start: 0.8680 (ptmt) cc_final: 0.8338 (mtpp) REVERT: G 31 MET cc_start: 0.8423 (mmt) cc_final: 0.7868 (mtt) REVERT: G 42 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7894 (mp) REVERT: G 68 CYS cc_start: 0.7953 (t) cc_final: 0.7519 (m) REVERT: G 126 THR cc_start: 0.9239 (t) cc_final: 0.8994 (p) REVERT: G 145 ASP cc_start: 0.8191 (p0) cc_final: 0.7958 (p0) REVERT: G 209 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7483 (tp30) REVERT: H 88 MET cc_start: 0.8838 (ttm) cc_final: 0.8589 (mtt) REVERT: H 115 ARG cc_start: 0.8617 (ptt-90) cc_final: 0.8297 (ptm160) REVERT: H 117 ASP cc_start: 0.8433 (m-30) cc_final: 0.7882 (p0) REVERT: H 244 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8738 (mp) REVERT: H 338 THR cc_start: 0.9457 (OUTLIER) cc_final: 0.9037 (p) REVERT: I 96 THR cc_start: 0.7302 (m) cc_final: 0.7099 (p) REVERT: I 199 TYR cc_start: 0.5505 (p90) cc_final: 0.5212 (p90) REVERT: I 325 MET cc_start: 0.8807 (ppp) cc_final: 0.8086 (ptt) REVERT: I 373 MET cc_start: 0.8156 (mtt) cc_final: 0.7870 (mtm) REVERT: J 50 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7440 (m-10) REVERT: J 158 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: J 196 LYS cc_start: 0.7986 (mttt) cc_final: 0.7582 (mtmt) REVERT: J 238 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8533 (t160) REVERT: J 250 ARG cc_start: 0.8096 (ptm160) cc_final: 0.7726 (ptm-80) REVERT: K 35 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: K 247 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: K 251 LYS cc_start: 0.8078 (ttpp) cc_final: 0.7795 (mtpp) REVERT: L 45 ARG cc_start: 0.8108 (tpp80) cc_final: 0.7791 (tpp80) REVERT: M 53 GLN cc_start: 0.7704 (tp40) cc_final: 0.7165 (tp40) REVERT: N 41 ASP cc_start: 0.7963 (m-30) cc_final: 0.7444 (m-30) REVERT: P 113 MET cc_start: 0.7071 (mmt) cc_final: 0.6594 (mmp) REVERT: P 253 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6767 (mtpt) REVERT: Q 111 MET cc_start: 0.5317 (tpt) cc_final: 0.4726 (ptt) REVERT: Q 255 MET cc_start: 0.6718 (mmm) cc_final: 0.6510 (tpt) REVERT: S 110 MET cc_start: 0.4377 (OUTLIER) cc_final: 0.3695 (ppp) REVERT: S 132 TRP cc_start: 0.8634 (m-10) cc_final: 0.8415 (m-10) REVERT: T 117 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7762 (mt-10) REVERT: T 139 ASP cc_start: 0.7350 (m-30) cc_final: 0.6902 (m-30) REVERT: T 144 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8158 (mp0) outliers start: 156 outliers final: 122 residues processed: 574 average time/residue: 0.4306 time to fit residues: 418.1409 Evaluate side-chains 567 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 434 time to evaluate : 4.042 ------------------------------------------------------------------------------- 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 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 280 MET Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 319 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 79 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 140 VAL 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 68 CYS Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 322 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 432 THR Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 LEU 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 271 CYS Chi-restraints excluded: chain G residue 291 VAL 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 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 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 236 THR Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 245 LYS Chi-restraints excluded: chain H residue 264 ASN Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 291 VAL Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 338 THR 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 40 GLU Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 362 TYR Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 169 MET 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 322 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 247 GLU Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 392 ARG 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 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain P residue 140 VAL 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 P residue 253 LYS Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain Q residue 170 CYS 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 118 ILE 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 297 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 322 optimal weight: 10.0000 chunk 338 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 423 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 232 HIS D 252 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 GLN J 238 ASN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.163225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117996 restraints weight = 46304.842| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.49 r_work: 0.3101 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 1.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 35724 Z= 0.231 Angle : 0.699 13.539 48732 Z= 0.355 Chirality : 0.048 0.300 5476 Planarity : 0.005 0.077 6244 Dihedral : 5.994 58.286 5548 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.68 % Favored : 92.20 % Rotamer: Outliers : 4.19 % Allowed : 19.86 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 4412 helix: 2.40 (0.23), residues: 544 sheet: -0.92 (0.14), residues: 1320 loop : -1.67 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 235 HIS 0.009 0.001 HIS E 116 PHE 0.036 0.002 PHE F 95 TYR 0.036 0.002 TYR B 305 ARG 0.007 0.001 ARG B 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 12) link_NAG-ASN : angle 2.36302 ( 36) link_BETA1-4 : bond 0.00795 ( 24) link_BETA1-4 : angle 2.24782 ( 72) hydrogen bonds : bond 0.03831 ( 991) hydrogen bonds : angle 5.15119 ( 2529) SS BOND : bond 0.00453 ( 68) SS BOND : angle 1.49352 ( 136) covalent geometry : bond 0.00571 (35620) covalent geometry : angle 0.68781 (48488) *********************** 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 601 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 443 time to evaluate : 3.894 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7559 (tptt) cc_final: 0.7332 (tttp) REVERT: A 88 MET cc_start: 0.8431 (ptp) cc_final: 0.8073 (ptm) REVERT: B 61 ASN cc_start: 0.8210 (m110) cc_final: 0.7869 (m-40) REVERT: B 76 GLU cc_start: 0.8123 (mp0) cc_final: 0.7724 (mp0) REVERT: B 119 ARG cc_start: 0.8845 (mpp80) cc_final: 0.8573 (mtm-85) REVERT: B 171 MET cc_start: 0.8981 (tpp) cc_final: 0.8770 (tpt) REVERT: B 250 ARG cc_start: 0.8384 (mmm-85) cc_final: 0.8175 (mmm-85) REVERT: B 373 MET cc_start: 0.7602 (mmt) cc_final: 0.6678 (mtm) REVERT: C 8 MET cc_start: 0.7361 (mpp) cc_final: 0.6743 (mpp) REVERT: C 53 GLN cc_start: 0.7830 (tt0) cc_final: 0.7161 (tp-100) REVERT: D 183 LYS cc_start: 0.8207 (pttt) cc_final: 0.7967 (ttpt) REVERT: F 1 TYR cc_start: 0.8623 (t80) cc_final: 0.8380 (t80) REVERT: F 79 LYS cc_start: 0.8495 (ptmt) cc_final: 0.8164 (ptpp) REVERT: F 115 ARG cc_start: 0.8755 (ptt-90) cc_final: 0.8368 (ptm-80) REVERT: F 182 ASP cc_start: 0.8785 (p0) cc_final: 0.8511 (p0) REVERT: F 351 LYS cc_start: 0.8708 (ptmt) cc_final: 0.8413 (mtpp) REVERT: G 31 MET cc_start: 0.8626 (mmt) cc_final: 0.8120 (mtt) REVERT: G 42 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.7943 (mp) REVERT: G 126 THR cc_start: 0.9264 (t) cc_final: 0.9007 (p) REVERT: G 209 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7561 (tp30) REVERT: H 115 ARG cc_start: 0.8706 (ptt-90) cc_final: 0.8424 (ptm160) REVERT: H 117 ASP cc_start: 0.8549 (m-30) cc_final: 0.7930 (p0) REVERT: H 244 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8773 (mp) REVERT: H 338 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.9081 (p) REVERT: I 199 TYR cc_start: 0.5862 (p90) cc_final: 0.5496 (p90) REVERT: I 325 MET cc_start: 0.9006 (ppp) cc_final: 0.8462 (ptt) REVERT: I 373 MET cc_start: 0.8226 (mtt) cc_final: 0.7923 (mtm) REVERT: J 50 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7559 (m-10) REVERT: J 53 GLN cc_start: 0.8730 (pt0) cc_final: 0.8530 (pt0) REVERT: J 158 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: J 178 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7987 (mmm-85) REVERT: J 196 LYS cc_start: 0.8008 (mttt) cc_final: 0.7625 (mtmt) REVERT: J 250 ARG cc_start: 0.8269 (ptm160) cc_final: 0.7977 (ptm-80) REVERT: K 35 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: K 247 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7404 (tp30) REVERT: L 45 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7976 (tpp80) REVERT: M 53 GLN cc_start: 0.7876 (tp40) cc_final: 0.7330 (tp40) REVERT: N 41 ASP cc_start: 0.7977 (m-30) cc_final: 0.7381 (m-30) REVERT: N 49 TYR cc_start: 0.7524 (m-80) cc_final: 0.7313 (m-80) REVERT: P 253 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6677 (mtpt) REVERT: Q 111 MET cc_start: 0.5355 (tpt) cc_final: 0.4736 (ptt) REVERT: Q 255 MET cc_start: 0.6726 (mmm) cc_final: 0.6514 (tpt) REVERT: E 133 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7825 (tpp80) REVERT: S 110 MET cc_start: 0.4630 (OUTLIER) cc_final: 0.3988 (ppp) REVERT: T 139 ASP cc_start: 0.7373 (m-30) cc_final: 0.6828 (m-30) REVERT: T 144 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8125 (mp0) outliers start: 158 outliers final: 131 residues processed: 574 average time/residue: 0.4647 time to fit residues: 452.9476 Evaluate side-chains 568 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 428 time to evaluate : 3.856 ------------------------------------------------------------------------------- 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 280 MET Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 330 VAL 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 53 GLN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 140 VAL 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 68 CYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 398 VAL Chi-restraints excluded: chain F residue 432 THR 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 42 LEU 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 210 SER 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 271 CYS Chi-restraints excluded: chain G residue 291 VAL 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 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 429 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 229 VAL Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 244 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 301 CYS Chi-restraints excluded: chain H residue 338 THR Chi-restraints excluded: chain H residue 339 LEU 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 40 GLU Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 362 TYR Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 220 CYS Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 247 GLU Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 392 ARG 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 135 LEU Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 253 LYS Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 140 VAL Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain S residue 110 MET Chi-restraints excluded: chain S residue 113 CYS Chi-restraints excluded: chain T residue 118 ILE Chi-restraints excluded: chain T residue 131 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 306 optimal weight: 0.9980 chunk 409 optimal weight: 5.9990 chunk 381 optimal weight: 20.0000 chunk 329 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 372 optimal weight: 30.0000 chunk 266 optimal weight: 2.9990 chunk 368 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN B 232 HIS J 53 GLN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN O 252 ASN E 126 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.165643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120513 restraints weight = 46153.590| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.50 r_work: 0.3140 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 1.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35724 Z= 0.136 Angle : 0.620 10.153 48732 Z= 0.312 Chirality : 0.045 0.239 5476 Planarity : 0.004 0.051 6244 Dihedral : 5.733 59.022 5548 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.26 % Favored : 93.63 % Rotamer: Outliers : 3.53 % Allowed : 20.60 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 4412 helix: 2.51 (0.23), residues: 544 sheet: -0.83 (0.14), residues: 1292 loop : -1.56 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 329 HIS 0.006 0.001 HIS E 116 PHE 0.034 0.001 PHE F 95 TYR 0.029 0.001 TYR K 64 ARG 0.007 0.000 ARG B 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 12) link_NAG-ASN : angle 2.17575 ( 36) link_BETA1-4 : bond 0.00815 ( 24) link_BETA1-4 : angle 2.17452 ( 72) hydrogen bonds : bond 0.03290 ( 991) hydrogen bonds : angle 4.99422 ( 2529) SS BOND : bond 0.00279 ( 68) SS BOND : angle 1.23013 ( 136) covalent geometry : bond 0.00330 (35620) covalent geometry : angle 0.60932 (48488) ********************** 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 581 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 448 time to evaluate : 4.092 Fit side-chains REVERT: B 76 GLU cc_start: 0.8124 (mp0) cc_final: 0.7827 (mp0) REVERT: B 119 ARG cc_start: 0.8835 (mpp80) cc_final: 0.8532 (mtm-85) REVERT: B 177 ASP cc_start: 0.8293 (p0) cc_final: 0.7908 (t0) REVERT: B 218 ASN cc_start: 0.6871 (t0) cc_final: 0.6140 (p0) REVERT: B 373 MET cc_start: 0.7553 (mmt) cc_final: 0.6722 (mtm) REVERT: C 8 MET cc_start: 0.7326 (mpp) cc_final: 0.6771 (mpp) REVERT: C 53 GLN cc_start: 0.7881 (tt0) cc_final: 0.7288 (tp-100) REVERT: D 122 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7454 (tm-30) REVERT: D 183 LYS cc_start: 0.8187 (pttt) cc_final: 0.7925 (ttpt) REVERT: F 79 LYS cc_start: 0.8447 (ptmt) cc_final: 0.8144 (ptpp) REVERT: F 115 ARG cc_start: 0.8701 (ptt-90) cc_final: 0.8378 (ptm-80) REVERT: F 182 ASP cc_start: 0.8757 (p0) cc_final: 0.8480 (p0) REVERT: F 351 LYS cc_start: 0.8700 (ptmt) cc_final: 0.8415 (mtpp) REVERT: G 31 MET cc_start: 0.8458 (mmt) cc_final: 0.8075 (mtt) REVERT: G 42 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7849 (mp) REVERT: G 68 CYS cc_start: 0.8210 (t) cc_final: 0.7659 (m) REVERT: G 126 THR cc_start: 0.9262 (t) cc_final: 0.9028 (p) REVERT: G 209 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7606 (tp30) REVERT: H 115 ARG cc_start: 0.8699 (ptt-90) cc_final: 0.8489 (ptm160) REVERT: H 117 ASP cc_start: 0.8520 (m-30) cc_final: 0.7951 (p0) REVERT: H 228 MET cc_start: 0.8771 (ttm) cc_final: 0.8497 (ttp) REVERT: H 321 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8260 (mtmm) REVERT: H 338 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9056 (p) REVERT: I 199 TYR cc_start: 0.6000 (p90) cc_final: 0.5564 (p90) REVERT: I 325 MET cc_start: 0.8785 (ppp) cc_final: 0.8204 (ptt) REVERT: I 373 MET cc_start: 0.8280 (mtt) cc_final: 0.7951 (mtm) REVERT: J 50 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7448 (m-10) REVERT: J 158 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: J 166 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8291 (mm-30) REVERT: J 196 LYS cc_start: 0.8141 (mttt) cc_final: 0.7759 (mtmt) REVERT: J 387 MET cc_start: 0.7634 (mtp) cc_final: 0.7350 (mtp) REVERT: K 35 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: L 45 ARG cc_start: 0.8332 (tpp80) cc_final: 0.8020 (tpp80) REVERT: M 53 GLN cc_start: 0.7891 (tp40) cc_final: 0.7298 (tp40) REVERT: N 41 ASP cc_start: 0.8069 (m-30) cc_final: 0.7447 (m-30) REVERT: P 253 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6776 (mtpt) REVERT: Q 111 MET cc_start: 0.5347 (tpt) cc_final: 0.4731 (ptt) REVERT: Q 255 MET cc_start: 0.6768 (mmm) cc_final: 0.6565 (tpt) REVERT: E 133 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7812 (tpp80) REVERT: S 110 MET cc_start: 0.4381 (OUTLIER) cc_final: 0.3699 (ppp) REVERT: T 110 MET cc_start: 0.6070 (ttm) cc_final: 0.5844 (ttm) REVERT: T 139 ASP cc_start: 0.7074 (m-30) cc_final: 0.6489 (m-30) REVERT: T 144 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8161 (mp0) outliers start: 133 outliers final: 113 residues processed: 555 average time/residue: 0.4333 time to fit residues: 404.0997 Evaluate side-chains 551 residues out of total 3772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 431 time to evaluate : 3.596 ------------------------------------------------------------------------------- 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 68 CYS Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 330 VAL 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 53 GLN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 140 VAL 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 68 CYS Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 322 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 G residue 19 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 338 THR 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 387 ILE 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 236 THR 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 301 CYS Chi-restraints excluded: chain H residue 338 THR 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 40 GLU Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 299 LEU 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 I residue 411 LEU Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 220 CYS Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 62 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 220 CYS 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 392 ARG Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 182 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 253 LYS Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 140 VAL 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 131 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 184 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 362 optimal weight: 50.0000 chunk 165 optimal weight: 3.9990 chunk 296 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 332 optimal weight: 0.0470 chunk 142 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 344 optimal weight: 3.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- 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 53 GLN B 184 GLN B 232 HIS ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN O 117 ASN O 252 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.164977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118698 restraints weight = 46321.611| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.49 r_work: 0.3132 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 1.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35724 Z= 0.156 Angle : 0.635 10.446 48732 Z= 0.320 Chirality : 0.045 0.308 5476 Planarity : 0.005 0.071 6244 Dihedral : 5.709 58.629 5548 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.98 % Favored : 92.91 % Rotamer: Outliers : 3.71 % Allowed : 20.65 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 4412 helix: 2.50 (0.23), residues: 548 sheet: -0.89 (0.14), residues: 1232 loop : -1.50 (0.12), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 235 HIS 0.006 0.001 HIS I 226 PHE 0.030 0.001 PHE F 95 TYR 0.038 0.002 TYR B 305 ARG 0.007 0.000 ARG B 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 12) link_NAG-ASN : angle 2.16500 ( 36) link_BETA1-4 : bond 0.00790 ( 24) link_BETA1-4 : angle 2.15650 ( 72) hydrogen bonds : bond 0.03342 ( 991) hydrogen bonds : angle 4.98515 ( 2529) SS BOND : bond 0.00286 ( 68) SS BOND : angle 1.28871 ( 136) covalent geometry : bond 0.00384 (35620) covalent geometry : angle 0.62479 (48488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26607.21 seconds wall clock time: 459 minutes 47.55 seconds (27587.55 seconds total)