Starting phenix.real_space_refine on Mon Aug 25 13:54:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrp_38609/08_2025/8xrp_38609.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrp_38609/08_2025/8xrp_38609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xrp_38609/08_2025/8xrp_38609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrp_38609/08_2025/8xrp_38609.map" model { file = "/net/cci-nas-00/data/ceres_data/8xrp_38609/08_2025/8xrp_38609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrp_38609/08_2025/8xrp_38609.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 18120 2.51 5 N 4868 2.21 5 O 5556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 245 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28740 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1485 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "B" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2413 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "C" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2335 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 276} Chain: "D" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "E" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1485 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "F" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2413 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "G" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2335 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 276} Chain: "H" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "I" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1485 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "J" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2413 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "K" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2335 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 276} Chain: "L" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "M" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1485 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "N" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2413 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "O" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2335 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 276} Chain: "P" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "Q" 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: "R" 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "K" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 5.96, per 1000 atoms: 0.21 Number of scatterers: 28740 At special positions: 0 Unit cell: (225.252, 121.758, 167.852, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 5556 8.00 N 4868 7.00 C 18120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=64, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS B 199 " distance=2.25 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 114 " distance=2.02 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 178 " distance=2.02 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 86 " distance=2.05 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS E 110 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 85 " - pdb=" SG CYS E 123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS F 199 " distance=2.25 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 142 " distance=2.04 Simple disulfide: pdb=" SG CYS F 170 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS F 300 " - pdb=" SG CYS F 327 " distance=2.03 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 51 " - pdb=" SG CYS G 101 " distance=2.03 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 105 " distance=2.04 Simple disulfide: pdb=" SG CYS G 132 " - pdb=" SG CYS G 143 " distance=2.03 Simple disulfide: pdb=" SG CYS G 173 " - pdb=" SG CYS G 178 " distance=2.02 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 62 " distance=2.03 Simple disulfide: pdb=" SG CYS H 80 " - pdb=" SG CYS H 86 " distance=2.05 Simple disulfide: pdb=" SG CYS I 37 " - pdb=" SG CYS I 110 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 85 " - pdb=" SG CYS I 123 " distance=2.03 Simple disulfide: pdb=" SG CYS I 96 " - pdb=" SG CYS J 199 " distance=2.25 Simple disulfide: pdb=" SG CYS J 50 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 142 " distance=2.04 Simple disulfide: pdb=" SG CYS J 170 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 300 " - pdb=" SG CYS J 327 " distance=2.03 Simple disulfide: pdb=" SG CYS K 28 " - pdb=" SG CYS K 114 " distance=2.04 Simple disulfide: pdb=" SG CYS K 51 " - pdb=" SG CYS K 101 " distance=2.03 Simple disulfide: pdb=" SG CYS K 59 " - pdb=" SG CYS K 105 " distance=2.04 Simple disulfide: pdb=" SG CYS K 132 " - pdb=" SG CYS K 143 " distance=2.03 Simple disulfide: pdb=" SG CYS K 173 " - pdb=" SG CYS K 178 " distance=2.02 Simple disulfide: pdb=" SG CYS L 29 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 52 " - pdb=" SG CYS L 62 " distance=2.03 Simple disulfide: pdb=" SG CYS L 80 " - pdb=" SG CYS L 86 " distance=2.05 Simple disulfide: pdb=" SG CYS M 37 " - pdb=" SG CYS M 110 " distance=2.03 Simple disulfide: pdb=" SG CYS M 64 " - pdb=" SG CYS M 196 " distance=2.03 Simple disulfide: pdb=" SG CYS M 85 " - pdb=" SG CYS M 123 " distance=2.03 Simple disulfide: pdb=" SG CYS M 96 " - pdb=" SG CYS N 199 " distance=2.25 Simple disulfide: pdb=" SG CYS N 50 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 142 " distance=2.04 Simple disulfide: pdb=" SG CYS N 170 " - pdb=" SG CYS N 193 " distance=2.03 Simple disulfide: pdb=" SG CYS N 300 " - pdb=" SG CYS N 327 " distance=2.03 Simple disulfide: pdb=" SG CYS O 28 " - pdb=" SG CYS O 114 " distance=2.04 Simple disulfide: pdb=" SG CYS O 51 " - pdb=" SG CYS O 101 " distance=2.03 Simple disulfide: pdb=" SG CYS O 59 " - pdb=" SG CYS O 105 " distance=2.04 Simple disulfide: pdb=" SG CYS O 132 " - pdb=" SG CYS O 143 " distance=2.03 Simple disulfide: pdb=" SG CYS O 173 " - pdb=" SG CYS O 178 " distance=2.02 Simple disulfide: pdb=" SG CYS P 29 " - pdb=" SG CYS P 87 " distance=2.03 Simple disulfide: pdb=" SG CYS P 52 " - pdb=" SG CYS P 62 " distance=2.03 Simple disulfide: pdb=" SG CYS P 80 " - pdb=" SG CYS P 86 " distance=2.05 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 Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " NAG-ASN " NAG C 401 " - " ASN C 48 " " NAG C 402 " - " ASN C 166 " " NAG C 403 " - " ASN C 195 " " NAG G 401 " - " ASN G 48 " " NAG G 402 " - " ASN G 166 " " NAG G 403 " - " ASN G 195 " " NAG K 401 " - " ASN K 48 " " NAG K 402 " - " ASN K 166 " " NAG K 403 " - " ASN K 195 " " NAG O 401 " - " ASN O 48 " " NAG O 402 " - " ASN O 166 " " NAG O 403 " - " ASN O 195 " " NAG Q 1 " - " ASN B 222 " " NAG R 1 " - " ASN F 222 " " NAG S 1 " - " ASN J 222 " " NAG T 1 " - " ASN N 222 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6800 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 75 sheets defined 14.6% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 117 through 147 removed outlier: 4.010A pdb=" N MET A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.937A pdb=" N THR A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'E' and resid 35 through 59 Processing helix chain 'E' and resid 80 through 85 Processing helix chain 'E' and resid 117 through 147 removed outlier: 4.009A pdb=" N MET E 147 " --> pdb=" O ALA E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 171 Processing helix chain 'E' and resid 187 through 218 removed outlier: 3.937A pdb=" N THR E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'F' and resid 228 through 233 Processing helix chain 'G' and resid 217 through 221 Processing helix chain 'H' and resid 100 through 104 Processing helix chain 'I' and resid 35 through 59 Processing helix chain 'I' and resid 80 through 85 Processing helix chain 'I' and resid 117 through 147 removed outlier: 4.010A pdb=" N MET I 147 " --> pdb=" O ALA I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 171 Processing helix chain 'I' and resid 187 through 218 removed outlier: 3.938A pdb=" N THR I 191 " --> pdb=" O ASP I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 85 Processing helix chain 'J' and resid 228 through 233 Processing helix chain 'K' and resid 217 through 221 Processing helix chain 'L' and resid 100 through 104 Processing helix chain 'M' and resid 35 through 59 Processing helix chain 'M' and resid 80 through 85 Processing helix chain 'M' and resid 117 through 147 removed outlier: 4.010A pdb=" N MET M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 171 Processing helix chain 'M' and resid 187 through 218 removed outlier: 3.938A pdb=" N THR M 191 " --> pdb=" O ASP M 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 228 through 233 Processing helix chain 'O' and resid 217 through 221 Processing helix chain 'P' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 removed outlier: 3.676A pdb=" N VAL G 141 " --> pdb=" O PHE G 183 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR G 140 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS G 135 " --> pdb=" O THR G 140 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ARG G 223 " --> pdb=" O CYS G 132 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN G 134 " --> pdb=" O ARG G 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE B 23 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 31 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS B 105 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 33 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS B 107 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 35 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS B 92 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 91 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 70 " --> pdb=" O TRP B 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE B 23 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 31 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS B 105 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 33 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS B 107 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 35 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 133 removed outlier: 6.526A pdb=" N GLU B 188 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain 'B' and resid 156 through 160 Processing sheet with id=AA8, first strand: chain 'B' and resid 239 through 245 removed outlier: 5.333A pdb=" N ASN B 240 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 257 " --> pdb=" O ASN B 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 289 through 291 removed outlier: 4.261A pdb=" N ALA B 304 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS B 327 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 31 through 34 Processing sheet with id=AB2, first strand: chain 'C' and resid 40 through 42 removed outlier: 5.754A pdb=" N ILE C 41 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN C 112 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU C 103 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS C 114 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 95 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU C 68 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE C 79 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU C 70 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 182 removed outlier: 7.658A pdb=" N ARG C 223 " --> pdb=" O CYS C 132 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN C 134 " --> pdb=" O ARG C 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU C 161 " --> pdb=" O TRP C 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU C 161 " --> pdb=" O TRP C 169 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 186 through 187 removed outlier: 5.362A pdb=" N ASN C 186 " --> pdb=" O SER E 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 232 through 233 Processing sheet with id=AB8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'D' and resid 47 through 56 removed outlier: 4.035A pdb=" N LEU D 50 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER D 63 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS D 52 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU D 61 " --> pdb=" O CYS D 52 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ARG D 54 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG D 59 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AC2, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.765A pdb=" N VAL D 111 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 23 through 27 removed outlier: 6.269A pdb=" N ILE F 23 " --> pdb=" O GLU F 34 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU F 25 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL F 32 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS F 27 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR F 31 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS F 105 " --> pdb=" O TYR F 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL F 33 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS F 107 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 35 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL F 96 " --> pdb=" O LYS F 92 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS F 92 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS F 91 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY F 70 " --> pdb=" O TRP F 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 23 through 27 removed outlier: 6.269A pdb=" N ILE F 23 " --> pdb=" O GLU F 34 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU F 25 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL F 32 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS F 27 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR F 31 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS F 105 " --> pdb=" O TYR F 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL F 33 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS F 107 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 35 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 47 through 49 Processing sheet with id=AC6, first strand: chain 'F' and resid 130 through 133 removed outlier: 6.525A pdb=" N GLU F 188 " --> pdb=" O SER F 176 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AC8, first strand: chain 'F' and resid 156 through 160 Processing sheet with id=AC9, first strand: chain 'F' and resid 239 through 245 removed outlier: 5.332A pdb=" N ASN F 240 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU F 257 " --> pdb=" O ASN F 240 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 289 through 291 removed outlier: 4.261A pdb=" N ALA F 304 " --> pdb=" O CYS F 327 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS F 327 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 31 through 34 Processing sheet with id=AD3, first strand: chain 'G' and resid 40 through 42 removed outlier: 5.755A pdb=" N ILE G 41 " --> pdb=" O GLY G 121 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN G 112 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU G 103 " --> pdb=" O GLN G 112 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS G 114 " --> pdb=" O CYS G 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY G 95 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU G 68 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE G 79 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU G 70 " --> pdb=" O ILE G 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 168 through 173 Processing sheet with id=AD5, first strand: chain 'G' and resid 168 through 173 Processing sheet with id=AD6, first strand: chain 'G' and resid 232 through 233 Processing sheet with id=AD7, first strand: chain 'G' and resid 256 through 257 Processing sheet with id=AD8, first strand: chain 'H' and resid 47 through 56 removed outlier: 4.034A pdb=" N LEU H 50 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER H 63 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYS H 52 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU H 61 " --> pdb=" O CYS H 52 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG H 54 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG H 59 " --> pdb=" O ARG H 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 87 through 88 Processing sheet with id=AE1, first strand: chain 'H' and resid 87 through 88 removed outlier: 3.764A pdb=" N VAL H 111 " --> pdb=" O LEU H 131 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 180 through 181 Processing sheet with id=AE3, first strand: chain 'J' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE J 23 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU J 34 " --> pdb=" O ILE J 23 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU J 25 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL J 32 " --> pdb=" O GLU J 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS J 27 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL J 96 " --> pdb=" O LYS J 92 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS J 92 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS J 91 " --> pdb=" O THR J 59 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY J 70 " --> pdb=" O TRP J 60 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE J 23 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU J 34 " --> pdb=" O ILE J 23 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU J 25 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL J 32 " --> pdb=" O GLU J 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS J 27 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 47 through 49 Processing sheet with id=AE6, first strand: chain 'J' and resid 130 through 133 removed outlier: 6.525A pdb=" N GLU J 188 " --> pdb=" O SER J 176 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 152 through 153 Processing sheet with id=AE8, first strand: chain 'J' and resid 156 through 160 Processing sheet with id=AE9, first strand: chain 'J' and resid 239 through 245 removed outlier: 5.332A pdb=" N ASN J 240 " --> pdb=" O GLU J 257 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU J 257 " --> pdb=" O ASN J 240 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 289 through 291 removed outlier: 4.263A pdb=" N ALA J 304 " --> pdb=" O CYS J 327 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS J 327 " --> pdb=" O ALA J 304 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE J 306 " --> pdb=" O VAL J 325 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 31 through 34 Processing sheet with id=AF3, first strand: chain 'K' and resid 40 through 42 removed outlier: 5.755A pdb=" N ILE K 41 " --> pdb=" O GLY K 121 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN K 112 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU K 103 " --> pdb=" O GLN K 112 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS K 114 " --> pdb=" O CYS K 101 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY K 95 " --> pdb=" O VAL K 120 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU K 68 " --> pdb=" O PHE K 79 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE K 79 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU K 70 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 181 through 182 removed outlier: 7.658A pdb=" N ARG K 223 " --> pdb=" O CYS K 132 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN K 134 " --> pdb=" O ARG K 223 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU K 161 " --> pdb=" O TRP K 169 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU K 161 " --> pdb=" O TRP K 169 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 186 through 187 removed outlier: 5.373A pdb=" N ASN K 186 " --> pdb=" O SER M 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'K' and resid 232 through 233 Processing sheet with id=AF9, first strand: chain 'K' and resid 256 through 257 Processing sheet with id=AG1, first strand: chain 'L' and resid 47 through 56 removed outlier: 4.036A pdb=" N LEU L 50 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER L 63 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS L 52 " --> pdb=" O GLU L 61 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU L 61 " --> pdb=" O CYS L 52 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG L 54 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG L 59 " --> pdb=" O ARG L 54 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 87 through 88 Processing sheet with id=AG3, first strand: chain 'L' and resid 87 through 88 removed outlier: 3.764A pdb=" N VAL L 111 " --> pdb=" O LEU L 131 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE N 23 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU N 34 " --> pdb=" O ILE N 23 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU N 25 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL N 32 " --> pdb=" O GLU N 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS N 27 " --> pdb=" O VAL N 30 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR N 31 " --> pdb=" O LEU N 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS N 105 " --> pdb=" O TYR N 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL N 33 " --> pdb=" O HIS N 105 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS N 107 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU N 35 " --> pdb=" O LYS N 107 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL N 96 " --> pdb=" O LYS N 92 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS N 92 " --> pdb=" O VAL N 96 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS N 91 " --> pdb=" O THR N 59 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY N 70 " --> pdb=" O TRP N 60 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE N 23 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU N 34 " --> pdb=" O ILE N 23 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU N 25 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL N 32 " --> pdb=" O GLU N 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS N 27 " --> pdb=" O VAL N 30 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR N 31 " --> pdb=" O LEU N 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS N 105 " --> pdb=" O TYR N 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL N 33 " --> pdb=" O HIS N 105 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS N 107 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU N 35 " --> pdb=" O LYS N 107 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 47 through 49 Processing sheet with id=AG7, first strand: chain 'N' and resid 130 through 133 removed outlier: 6.525A pdb=" N GLU N 188 " --> pdb=" O SER N 176 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 152 through 153 Processing sheet with id=AG9, first strand: chain 'N' and resid 156 through 160 Processing sheet with id=AH1, first strand: chain 'N' and resid 239 through 245 removed outlier: 5.332A pdb=" N ASN N 240 " --> pdb=" O GLU N 257 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU N 257 " --> pdb=" O ASN N 240 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 289 through 291 removed outlier: 4.263A pdb=" N ALA N 304 " --> pdb=" O CYS N 327 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS N 327 " --> pdb=" O ALA N 304 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE N 306 " --> pdb=" O VAL N 325 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 31 through 34 Processing sheet with id=AH4, first strand: chain 'O' and resid 40 through 42 removed outlier: 5.757A pdb=" N ILE O 41 " --> pdb=" O GLY O 121 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN O 112 " --> pdb=" O LEU O 103 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU O 103 " --> pdb=" O GLN O 112 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS O 114 " --> pdb=" O CYS O 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY O 95 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU O 68 " --> pdb=" O PHE O 79 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE O 79 " --> pdb=" O LEU O 68 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU O 70 " --> pdb=" O ILE O 77 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 181 through 182 removed outlier: 7.658A pdb=" N ARG O 223 " --> pdb=" O CYS O 132 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN O 134 " --> pdb=" O ARG O 223 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU O 161 " --> pdb=" O TRP O 169 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 168 through 173 removed outlier: 3.505A pdb=" N LEU O 161 " --> pdb=" O TRP O 169 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 232 through 233 Processing sheet with id=AH9, first strand: chain 'O' and resid 256 through 257 Processing sheet with id=AI1, first strand: chain 'P' and resid 47 through 56 removed outlier: 4.035A pdb=" N LEU P 50 " --> pdb=" O SER P 63 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER P 63 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS P 52 " --> pdb=" O GLU P 61 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU P 61 " --> pdb=" O CYS P 52 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ARG P 54 " --> pdb=" O ARG P 59 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG P 59 " --> pdb=" O ARG P 54 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P' and resid 87 through 88 Processing sheet with id=AI3, first strand: chain 'P' and resid 87 through 88 removed outlier: 3.764A pdb=" N VAL P 111 " --> pdb=" O LEU P 131 " (cutoff:3.500A) 1013 hydrogen bonds defined for protein. 2652 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: 4.94 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5466 1.32 - 1.45: 7313 1.45 - 1.57: 16357 1.57 - 1.69: 0 1.69 - 1.82: 248 Bond restraints: 29384 Sorted by residual: bond pdb=" CA VAL D 107 " pdb=" CB VAL D 107 " ideal model delta sigma weight residual 1.537 1.479 0.058 1.24e-02 6.50e+03 2.22e+01 bond pdb=" CA PRO J 237 " pdb=" C PRO J 237 " ideal model delta sigma weight residual 1.514 1.538 -0.024 5.50e-03 3.31e+04 1.90e+01 bond pdb=" CA LYS C 165 " pdb=" C LYS C 165 " ideal model delta sigma weight residual 1.528 1.476 0.053 1.28e-02 6.10e+03 1.71e+01 bond pdb=" CA PRO F 237 " pdb=" C PRO F 237 " ideal model delta sigma weight residual 1.514 1.537 -0.023 5.50e-03 3.31e+04 1.69e+01 bond pdb=" CA PRO N 237 " pdb=" C PRO N 237 " ideal model delta sigma weight residual 1.514 1.537 -0.023 5.50e-03 3.31e+04 1.68e+01 ... (remaining 29379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 33526 2.30 - 4.60: 6070 4.60 - 6.90: 190 6.90 - 9.20: 23 9.20 - 11.50: 7 Bond angle restraints: 39816 Sorted by residual: angle pdb=" N LYS G 165 " pdb=" CA LYS G 165 " pdb=" C LYS G 165 " ideal model delta sigma weight residual 110.35 98.85 11.50 1.38e+00 5.25e-01 6.94e+01 angle pdb=" N ARG G 65 " pdb=" CA ARG G 65 " pdb=" C ARG G 65 " ideal model delta sigma weight residual 114.62 106.79 7.83 1.14e+00 7.69e-01 4.72e+01 angle pdb=" N ARG O 65 " pdb=" CA ARG O 65 " pdb=" C ARG O 65 " ideal model delta sigma weight residual 114.62 106.82 7.80 1.14e+00 7.69e-01 4.68e+01 angle pdb=" N ARG K 65 " pdb=" CA ARG K 65 " pdb=" C ARG K 65 " ideal model delta sigma weight residual 114.62 106.82 7.80 1.14e+00 7.69e-01 4.68e+01 angle pdb=" N ARG C 65 " pdb=" CA ARG C 65 " pdb=" C ARG C 65 " ideal model delta sigma weight residual 114.62 106.86 7.76 1.14e+00 7.69e-01 4.63e+01 ... (remaining 39811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.21: 16980 20.21 - 40.41: 1029 40.41 - 60.62: 186 60.62 - 80.83: 32 80.83 - 101.03: 21 Dihedral angle restraints: 18248 sinusoidal: 7772 harmonic: 10476 Sorted by residual: dihedral pdb=" CB CYS K 59 " pdb=" SG CYS K 59 " pdb=" SG CYS K 105 " pdb=" CB CYS K 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.33 -73.33 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" CB CYS G 59 " pdb=" SG CYS G 59 " pdb=" SG CYS G 105 " pdb=" CB CYS G 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.26 -73.26 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS C 59 " pdb=" SG CYS C 59 " pdb=" SG CYS C 105 " pdb=" CB CYS C 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.23 -73.23 1 1.00e+01 1.00e-02 6.83e+01 ... (remaining 18245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2035 0.076 - 0.151: 1624 0.151 - 0.227: 619 0.227 - 0.302: 184 0.302 - 0.377: 22 Chirality restraints: 4484 Sorted by residual: chirality pdb=" CA THR P 123 " pdb=" N THR P 123 " pdb=" C THR P 123 " pdb=" CB THR P 123 " both_signs ideal model delta sigma weight residual False 2.53 2.90 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA THR D 123 " pdb=" N THR D 123 " pdb=" C THR D 123 " pdb=" CB THR D 123 " both_signs ideal model delta sigma weight residual False 2.53 2.90 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA THR H 123 " pdb=" N THR H 123 " pdb=" C THR H 123 " pdb=" CB THR H 123 " both_signs ideal model delta sigma weight residual False 2.53 2.90 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 4481 not shown) Planarity restraints: 5048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 100 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C SER D 100 " 0.052 2.00e-02 2.50e+03 pdb=" O SER D 100 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP D 101 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 196 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C ASP F 196 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP F 196 " 0.019 2.00e-02 2.50e+03 pdb=" N SER F 197 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP N 196 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C ASP N 196 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP N 196 " -0.019 2.00e-02 2.50e+03 pdb=" N SER N 197 " -0.018 2.00e-02 2.50e+03 ... (remaining 5045 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 659 2.68 - 3.23: 25146 3.23 - 3.79: 41409 3.79 - 4.34: 59167 4.34 - 4.90: 93834 Nonbonded interactions: 220215 Sorted by model distance: nonbonded pdb=" CD2 LEU J 117 " pdb=" CG2 THR J 146 " model vdw 2.120 3.880 nonbonded pdb=" CD2 LEU B 117 " pdb=" CG2 THR B 146 " model vdw 2.121 3.880 nonbonded pdb=" CD2 LEU F 117 " pdb=" CG2 THR F 146 " model vdw 2.122 3.880 nonbonded pdb=" CD2 LEU N 117 " pdb=" CG2 THR N 146 " model vdw 2.122 3.880 nonbonded pdb=" N LYS G 165 " pdb=" O LYS G 165 " model vdw 2.333 2.496 ... (remaining 220210 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.300 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.013 0.217 29472 Z= 0.994 Angle : 1.626 29.655 40016 Z= 1.209 Chirality : 0.114 0.377 4484 Planarity : 0.004 0.030 5032 Dihedral : 13.235 101.032 11256 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.92 % Allowed : 9.89 % Favored : 88.18 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.14), residues: 3520 helix: 2.86 (0.24), residues: 500 sheet: 0.92 (0.16), residues: 1164 loop : -0.58 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 260 TYR 0.025 0.002 TYR J 268 PHE 0.027 0.002 PHE P 99 TRP 0.028 0.002 TRP N 60 HIS 0.004 0.001 HIS N 266 Details of bonding type rmsd covalent geometry : bond 0.01296 (29384) covalent geometry : angle 1.59113 (39816) SS BOND : bond 0.05447 ( 64) SS BOND : angle 5.53959 ( 128) hydrogen bonds : bond 0.21044 ( 918) hydrogen bonds : angle 8.71370 ( 2652) link_BETA1-4 : bond 0.01272 ( 8) link_BETA1-4 : angle 2.26920 ( 24) link_NAG-ASN : bond 0.01173 ( 16) link_NAG-ASN : angle 4.30537 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 626 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7950 (t0) cc_final: 0.7445 (t0) REVERT: B 240 ASN cc_start: 0.7430 (t0) cc_final: 0.7222 (t0) REVERT: C 251 LEU cc_start: 0.8606 (mt) cc_final: 0.8037 (tt) REVERT: D 58 ASP cc_start: 0.7685 (p0) cc_final: 0.7420 (p0) REVERT: D 64 TRP cc_start: 0.5470 (p90) cc_final: 0.3437 (p90) REVERT: D 123 THR cc_start: 0.6044 (m) cc_final: 0.5762 (p) REVERT: F 82 PHE cc_start: 0.3553 (m-80) cc_final: 0.3347 (m-80) REVERT: G 41 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8320 (pt) REVERT: G 251 LEU cc_start: 0.8511 (mt) cc_final: 0.8258 (tt) REVERT: G 253 LEU cc_start: 0.8037 (mt) cc_final: 0.7788 (mm) REVERT: J 191 VAL cc_start: 0.7769 (p) cc_final: 0.7460 (p) REVERT: K 228 TRP cc_start: 0.6244 (p-90) cc_final: 0.5782 (p90) REVERT: K 249 GLU cc_start: 0.7040 (mm-30) cc_final: 0.5783 (mm-30) REVERT: N 32 VAL cc_start: 0.6789 (t) cc_final: 0.5735 (t) outliers start: 62 outliers final: 11 residues processed: 676 average time/residue: 0.1714 time to fit residues: 180.4001 Evaluate side-chains 302 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 290 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 276 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN B 91 HIS B 105 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN C 268 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN G 268 ASN H 102 GLN I 42 GLN I 57 GLN I 152 GLN J 87 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN K 255 ASN K 268 ASN L 102 GLN M 168 GLN N 87 GLN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 255 ASN O 268 ASN P 102 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.174930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.147783 restraints weight = 58681.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.140448 restraints weight = 83521.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.138743 restraints weight = 87589.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.139079 restraints weight = 75027.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.138559 restraints weight = 59365.821| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29472 Z= 0.227 Angle : 0.709 10.464 40016 Z= 0.371 Chirality : 0.045 0.250 4484 Planarity : 0.005 0.075 5032 Dihedral : 7.594 59.709 4382 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.13 % Allowed : 14.61 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.14), residues: 3520 helix: 2.82 (0.23), residues: 472 sheet: 0.92 (0.15), residues: 1220 loop : -0.70 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 309 TYR 0.028 0.002 TYR J 314 PHE 0.026 0.002 PHE B 228 TRP 0.032 0.002 TRP C 228 HIS 0.013 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00536 (29384) covalent geometry : angle 0.69231 (39816) SS BOND : bond 0.00385 ( 64) SS BOND : angle 1.84660 ( 128) hydrogen bonds : bond 0.06116 ( 918) hydrogen bonds : angle 5.80158 ( 2652) link_BETA1-4 : bond 0.00926 ( 8) link_BETA1-4 : angle 2.12706 ( 24) link_NAG-ASN : bond 0.00519 ( 16) link_NAG-ASN : angle 3.21767 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 324 time to evaluate : 1.197 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: A 34 MET cc_start: 0.7126 (tmm) cc_final: 0.6624 (tpp) REVERT: A 88 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8139 (mm) REVERT: A 157 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6814 (mp10) REVERT: A 210 ASP cc_start: 0.8468 (t0) cc_final: 0.7891 (t0) REVERT: B 59 THR cc_start: 0.4654 (OUTLIER) cc_final: 0.4378 (p) REVERT: C 137 GLU cc_start: 0.6811 (pt0) cc_final: 0.4953 (pt0) REVERT: F 194 GLN cc_start: 0.6808 (tm-30) cc_final: 0.6578 (tm-30) REVERT: G 259 TYR cc_start: 0.5649 (p90) cc_final: 0.5290 (p90) REVERT: I 73 ASP cc_start: 0.7752 (t70) cc_final: 0.7410 (t0) REVERT: I 152 GLN cc_start: 0.7992 (tt0) cc_final: 0.7790 (tt0) REVERT: J 104 LEU cc_start: 0.6462 (mt) cc_final: 0.5992 (tt) REVERT: J 194 GLN cc_start: 0.7391 (tm-30) cc_final: 0.7087 (tm-30) REVERT: M 88 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7217 (mm) REVERT: M 133 MET cc_start: 0.7468 (mtp) cc_final: 0.7159 (mtp) REVERT: M 164 ASP cc_start: 0.8121 (t0) cc_final: 0.7883 (t0) REVERT: M 175 GLU cc_start: 0.7075 (tp30) cc_final: 0.6790 (tp30) REVERT: N 166 GLN cc_start: 0.5442 (tp-100) cc_final: 0.5239 (tp40) REVERT: N 204 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7252 (mt-10) outliers start: 101 outliers final: 53 residues processed: 404 average time/residue: 0.1660 time to fit residues: 106.4202 Evaluate side-chains 317 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 260 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 MET Chi-restraints excluded: chain J residue 170 CYS Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 250 ARG Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 321 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 313 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 285 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN F 87 GLN ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 GLN I 168 GLN J 248 ASN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN K 299 HIS M 53 GLN M 57 GLN M 168 GLN ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** N 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.174897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.148329 restraints weight = 58603.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.141997 restraints weight = 79330.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.139143 restraints weight = 76090.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.138708 restraints weight = 72047.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.138664 restraints weight = 56645.097| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29472 Z= 0.130 Angle : 0.563 8.187 40016 Z= 0.294 Chirality : 0.040 0.223 4484 Planarity : 0.004 0.038 5032 Dihedral : 5.938 53.982 4376 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 2.73 % Allowed : 15.66 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.14), residues: 3520 helix: 2.87 (0.22), residues: 472 sheet: 0.94 (0.15), residues: 1208 loop : -0.71 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 48 TYR 0.018 0.001 TYR G 71 PHE 0.019 0.001 PHE E 118 TRP 0.029 0.001 TRP J 24 HIS 0.005 0.001 HIS F 266 Details of bonding type rmsd covalent geometry : bond 0.00296 (29384) covalent geometry : angle 0.54881 (39816) SS BOND : bond 0.00225 ( 64) SS BOND : angle 1.48687 ( 128) hydrogen bonds : bond 0.05240 ( 918) hydrogen bonds : angle 5.18078 ( 2652) link_BETA1-4 : bond 0.00852 ( 8) link_BETA1-4 : angle 1.62674 ( 24) link_NAG-ASN : bond 0.00178 ( 16) link_NAG-ASN : angle 2.74167 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 291 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7102 (tmm) cc_final: 0.6640 (tpp) REVERT: A 88 LEU cc_start: 0.8306 (pt) cc_final: 0.7986 (mm) REVERT: A 157 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6817 (mp10) REVERT: A 210 ASP cc_start: 0.8564 (t0) cc_final: 0.8118 (t0) REVERT: E 210 ASP cc_start: 0.7841 (t70) cc_final: 0.6548 (t0) REVERT: F 220 TYR cc_start: 0.5989 (t80) cc_final: 0.4817 (t80) REVERT: F 314 TYR cc_start: 0.8591 (m-10) cc_final: 0.8279 (m-10) REVERT: I 73 ASP cc_start: 0.7723 (t70) cc_final: 0.7359 (t0) REVERT: J 104 LEU cc_start: 0.6327 (mt) cc_final: 0.5964 (tt) REVERT: J 194 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7130 (tm-30) REVERT: M 88 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6991 (mm) REVERT: M 120 MET cc_start: 0.7185 (mmp) cc_final: 0.6641 (mmp) REVERT: M 133 MET cc_start: 0.7354 (mtp) cc_final: 0.7108 (mtp) REVERT: O 228 TRP cc_start: 0.6777 (p-90) cc_final: 0.6078 (p-90) outliers start: 88 outliers final: 48 residues processed: 353 average time/residue: 0.1823 time to fit residues: 102.9993 Evaluate side-chains 299 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 249 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain I residue 119 MET Chi-restraints excluded: chain I residue 168 GLN Chi-restraints excluded: chain J residue 170 CYS Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 250 ARG Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain O residue 60 PHE Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 269 MET Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 151 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 326 optimal weight: 0.0470 chunk 257 optimal weight: 30.0000 chunk 93 optimal weight: 8.9990 chunk 340 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN G 66 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN M 168 GLN ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN O 134 GLN ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.162165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118675 restraints weight = 54951.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.114355 restraints weight = 67947.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115245 restraints weight = 62617.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.115530 restraints weight = 53885.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115585 restraints weight = 51035.888| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 29472 Z= 0.254 Angle : 0.668 11.646 40016 Z= 0.349 Chirality : 0.043 0.284 4484 Planarity : 0.005 0.063 5032 Dihedral : 5.506 46.301 4373 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.85 % Allowed : 15.79 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.14), residues: 3520 helix: 2.34 (0.23), residues: 460 sheet: 0.72 (0.15), residues: 1232 loop : -0.85 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 48 TYR 0.022 0.002 TYR J 268 PHE 0.026 0.002 PHE O 73 TRP 0.036 0.002 TRP B 60 HIS 0.007 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00606 (29384) covalent geometry : angle 0.65230 (39816) SS BOND : bond 0.00767 ( 64) SS BOND : angle 1.88965 ( 128) hydrogen bonds : bond 0.05963 ( 918) hydrogen bonds : angle 5.28101 ( 2652) link_BETA1-4 : bond 0.00666 ( 8) link_BETA1-4 : angle 1.50129 ( 24) link_NAG-ASN : bond 0.00421 ( 16) link_NAG-ASN : angle 2.97877 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 272 time to evaluate : 0.866 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: A 34 MET cc_start: 0.7366 (tmm) cc_final: 0.6939 (tpp) REVERT: A 88 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8034 (mm) REVERT: A 119 MET cc_start: 0.8595 (tpt) cc_final: 0.8395 (tpt) REVERT: A 157 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: A 164 ASP cc_start: 0.8158 (t0) cc_final: 0.7930 (m-30) REVERT: A 210 ASP cc_start: 0.8565 (t0) cc_final: 0.8118 (t0) REVERT: E 210 ASP cc_start: 0.8214 (t70) cc_final: 0.7994 (t0) REVERT: F 117 LEU cc_start: 0.5533 (OUTLIER) cc_final: 0.4979 (mm) REVERT: G 190 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: G 253 LEU cc_start: 0.8220 (mm) cc_final: 0.7540 (tp) REVERT: H 93 SER cc_start: 0.0373 (OUTLIER) cc_final: 0.0150 (p) REVERT: J 194 GLN cc_start: 0.7506 (tm-30) cc_final: 0.6940 (tm-30) REVERT: J 313 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7840 (ttt90) REVERT: M 88 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7269 (mm) REVERT: N 117 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7566 (mm) REVERT: N 166 GLN cc_start: 0.6038 (tp40) cc_final: 0.5813 (tp40) outliers start: 124 outliers final: 68 residues processed: 371 average time/residue: 0.1752 time to fit residues: 102.4822 Evaluate side-chains 319 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 243 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 277 VAL Chi-restraints excluded: chain J residue 313 ARG Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 179 ARG Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 66 ASN Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 269 MET Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 200 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 246 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 286 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 192 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN G 66 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 HIS ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.160495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112148 restraints weight = 55651.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108134 restraints weight = 46167.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108492 restraints weight = 46040.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108924 restraints weight = 44446.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109113 restraints weight = 39772.237| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 29472 Z= 0.191 Angle : 0.583 11.693 40016 Z= 0.304 Chirality : 0.041 0.267 4484 Planarity : 0.004 0.038 5032 Dihedral : 5.228 47.222 4373 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.13 % Allowed : 16.75 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.14), residues: 3520 helix: 2.47 (0.23), residues: 460 sheet: 0.80 (0.15), residues: 1180 loop : -0.92 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 64 TYR 0.022 0.002 TYR G 71 PHE 0.023 0.002 PHE J 128 TRP 0.022 0.002 TRP B 60 HIS 0.007 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00453 (29384) covalent geometry : angle 0.56958 (39816) SS BOND : bond 0.00325 ( 64) SS BOND : angle 1.53985 ( 128) hydrogen bonds : bond 0.05251 ( 918) hydrogen bonds : angle 4.99969 ( 2652) link_BETA1-4 : bond 0.00726 ( 8) link_BETA1-4 : angle 1.44131 ( 24) link_NAG-ASN : bond 0.00146 ( 16) link_NAG-ASN : angle 2.58209 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 254 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7360 (tmm) cc_final: 0.6975 (tpp) REVERT: A 88 LEU cc_start: 0.8441 (pt) cc_final: 0.8021 (mm) REVERT: A 157 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: A 164 ASP cc_start: 0.8278 (t0) cc_final: 0.8041 (m-30) REVERT: A 210 ASP cc_start: 0.8503 (t0) cc_final: 0.8192 (t0) REVERT: D 58 ASP cc_start: 0.7229 (t0) cc_final: 0.6945 (t0) REVERT: E 210 ASP cc_start: 0.8314 (t70) cc_final: 0.8064 (t0) REVERT: F 117 LEU cc_start: 0.5070 (OUTLIER) cc_final: 0.4531 (mm) REVERT: G 253 LEU cc_start: 0.8367 (mm) cc_final: 0.7614 (tp) REVERT: J 194 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6595 (tm-30) REVERT: M 120 MET cc_start: 0.7260 (mmp) cc_final: 0.6873 (mmp) REVERT: N 117 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7172 (mm) REVERT: N 223 TYR cc_start: 0.7139 (m-80) cc_final: 0.6747 (m-80) outliers start: 101 outliers final: 70 residues processed: 330 average time/residue: 0.1683 time to fit residues: 87.8693 Evaluate side-chains 311 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 238 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 269 MET Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 348 optimal weight: 0.3980 chunk 96 optimal weight: 9.9990 chunk 300 optimal weight: 2.9990 chunk 318 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 chunk 346 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 256 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN M 168 GLN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.160197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111776 restraints weight = 55099.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.108092 restraints weight = 44755.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108450 restraints weight = 43881.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108995 restraints weight = 41405.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108970 restraints weight = 38291.252| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29472 Z= 0.179 Angle : 0.575 13.204 40016 Z= 0.299 Chirality : 0.040 0.269 4484 Planarity : 0.004 0.042 5032 Dihedral : 5.074 50.560 4373 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.44 % Allowed : 16.81 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.14), residues: 3520 helix: 2.55 (0.23), residues: 460 sheet: 0.74 (0.15), residues: 1180 loop : -0.94 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 64 TYR 0.022 0.001 TYR O 71 PHE 0.024 0.002 PHE J 128 TRP 0.029 0.002 TRP F 24 HIS 0.007 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00424 (29384) covalent geometry : angle 0.56219 (39816) SS BOND : bond 0.00549 ( 64) SS BOND : angle 1.47748 ( 128) hydrogen bonds : bond 0.05125 ( 918) hydrogen bonds : angle 4.88134 ( 2652) link_BETA1-4 : bond 0.00768 ( 8) link_BETA1-4 : angle 1.44568 ( 24) link_NAG-ASN : bond 0.00196 ( 16) link_NAG-ASN : angle 2.53150 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 245 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7280 (tmm) cc_final: 0.6942 (tpp) REVERT: A 88 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8041 (mm) REVERT: A 119 MET cc_start: 0.8672 (tpt) cc_final: 0.8391 (tpt) REVERT: A 157 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7419 (mp10) REVERT: A 164 ASP cc_start: 0.8261 (t0) cc_final: 0.8047 (m-30) REVERT: B 192 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: D 48 ARG cc_start: 0.7598 (mmp80) cc_final: 0.7016 (mmp80) REVERT: D 58 ASP cc_start: 0.7075 (t0) cc_final: 0.6842 (t0) REVERT: E 210 ASP cc_start: 0.8346 (t70) cc_final: 0.8096 (t0) REVERT: F 26 LEU cc_start: 0.6412 (tp) cc_final: 0.6191 (tp) REVERT: F 117 LEU cc_start: 0.5103 (OUTLIER) cc_final: 0.4600 (mm) REVERT: F 139 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6826 (ttm110) REVERT: G 253 LEU cc_start: 0.8365 (mm) cc_final: 0.7590 (tp) REVERT: J 82 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.5729 (m-80) REVERT: J 194 GLN cc_start: 0.7263 (tm-30) cc_final: 0.6580 (tm-30) REVERT: M 120 MET cc_start: 0.7271 (mmp) cc_final: 0.6903 (mmp) REVERT: N 117 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7167 (mm) REVERT: N 166 GLN cc_start: 0.6395 (tp40) cc_final: 0.6171 (tp40) REVERT: N 223 TYR cc_start: 0.7183 (m-80) cc_final: 0.6757 (m-80) outliers start: 111 outliers final: 82 residues processed: 331 average time/residue: 0.1629 time to fit residues: 86.1415 Evaluate side-chains 325 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 236 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 82 PHE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 170 CYS Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 269 MET Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 232 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 323 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 257 optimal weight: 0.3980 chunk 44 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN F 166 GLN G 66 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.160757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3517 r_free = 0.3517 target = 0.112717 restraints weight = 55106.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108414 restraints weight = 45389.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109005 restraints weight = 43835.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109227 restraints weight = 40774.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109349 restraints weight = 37693.668| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29472 Z= 0.142 Angle : 0.540 12.234 40016 Z= 0.280 Chirality : 0.039 0.242 4484 Planarity : 0.003 0.038 5032 Dihedral : 4.875 50.549 4373 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.23 % Allowed : 17.18 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.14), residues: 3520 helix: 2.66 (0.23), residues: 460 sheet: 0.76 (0.15), residues: 1176 loop : -0.88 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 114 TYR 0.018 0.001 TYR F 220 PHE 0.018 0.001 PHE N 128 TRP 0.033 0.001 TRP F 24 HIS 0.007 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00334 (29384) covalent geometry : angle 0.52784 (39816) SS BOND : bond 0.00322 ( 64) SS BOND : angle 1.38740 ( 128) hydrogen bonds : bond 0.04736 ( 918) hydrogen bonds : angle 4.69400 ( 2652) link_BETA1-4 : bond 0.00756 ( 8) link_BETA1-4 : angle 1.41393 ( 24) link_NAG-ASN : bond 0.00115 ( 16) link_NAG-ASN : angle 2.33636 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 242 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7291 (tmm) cc_final: 0.6937 (tpp) REVERT: A 88 LEU cc_start: 0.8427 (pt) cc_final: 0.8053 (mm) REVERT: A 119 MET cc_start: 0.8630 (tpt) cc_final: 0.8390 (tpt) REVERT: A 157 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: A 164 ASP cc_start: 0.8198 (t0) cc_final: 0.7980 (m-30) REVERT: B 157 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8345 (mtmm) REVERT: E 210 ASP cc_start: 0.8349 (t70) cc_final: 0.8077 (t0) REVERT: F 117 LEU cc_start: 0.4971 (OUTLIER) cc_final: 0.4475 (mm) REVERT: I 119 MET cc_start: 0.7278 (tpp) cc_final: 0.7021 (tpp) REVERT: J 82 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.5774 (m-80) REVERT: J 130 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.6290 (ttp-110) REVERT: J 194 GLN cc_start: 0.7216 (tm-30) cc_final: 0.6541 (tm-30) REVERT: K 253 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8454 (tt) REVERT: M 120 MET cc_start: 0.7219 (mmp) cc_final: 0.6893 (mmp) REVERT: N 117 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7123 (mm) REVERT: N 166 GLN cc_start: 0.6233 (tp40) cc_final: 0.5903 (tp40) REVERT: N 223 TYR cc_start: 0.7117 (m-80) cc_final: 0.6687 (m-80) outliers start: 104 outliers final: 80 residues processed: 330 average time/residue: 0.1713 time to fit residues: 89.6394 Evaluate side-chains 318 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 231 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain J residue 82 PHE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 66 ASN Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 269 MET Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 319 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 157 optimal weight: 9.9990 chunk 326 optimal weight: 1.9990 chunk 347 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 299 optimal weight: 7.9990 chunk 335 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.160085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.111711 restraints weight = 55592.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.107917 restraints weight = 46864.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108272 restraints weight = 45064.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108565 restraints weight = 43685.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.108750 restraints weight = 40164.792| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29472 Z= 0.160 Angle : 0.553 14.650 40016 Z= 0.286 Chirality : 0.039 0.253 4484 Planarity : 0.003 0.038 5032 Dihedral : 4.863 51.130 4373 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.19 % Allowed : 17.21 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.14), residues: 3520 helix: 2.66 (0.23), residues: 460 sheet: 0.75 (0.15), residues: 1152 loop : -0.92 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 114 TYR 0.020 0.001 TYR I 215 PHE 0.019 0.002 PHE F 82 TRP 0.028 0.001 TRP B 60 HIS 0.006 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00379 (29384) covalent geometry : angle 0.54225 (39816) SS BOND : bond 0.00280 ( 64) SS BOND : angle 1.26774 ( 128) hydrogen bonds : bond 0.04859 ( 918) hydrogen bonds : angle 4.69021 ( 2652) link_BETA1-4 : bond 0.00686 ( 8) link_BETA1-4 : angle 1.39351 ( 24) link_NAG-ASN : bond 0.00144 ( 16) link_NAG-ASN : angle 2.39637 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 242 time to evaluate : 0.769 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: A 34 MET cc_start: 0.7243 (tmm) cc_final: 0.6925 (tpp) REVERT: A 77 ASP cc_start: 0.7801 (p0) cc_final: 0.7584 (p0) REVERT: A 88 LEU cc_start: 0.8456 (pt) cc_final: 0.8069 (mm) REVERT: A 157 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: B 31 TYR cc_start: 0.7298 (m-80) cc_final: 0.7025 (m-80) REVERT: B 157 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8377 (mtmm) REVERT: D 48 ARG cc_start: 0.7531 (mmp80) cc_final: 0.6964 (mmp80) REVERT: D 125 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7485 (mptt) REVERT: E 210 ASP cc_start: 0.8359 (t70) cc_final: 0.8128 (t70) REVERT: F 117 LEU cc_start: 0.5073 (OUTLIER) cc_final: 0.4596 (mm) REVERT: F 139 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6828 (ttm110) REVERT: I 119 MET cc_start: 0.7247 (tpp) cc_final: 0.7010 (tpp) REVERT: J 82 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.5630 (m-80) REVERT: J 194 GLN cc_start: 0.7270 (tm-30) cc_final: 0.6574 (tm-30) REVERT: M 120 MET cc_start: 0.7348 (mmp) cc_final: 0.6985 (mmp) REVERT: N 117 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7236 (mm) REVERT: N 166 GLN cc_start: 0.6203 (tp40) cc_final: 0.5980 (tp40) REVERT: N 223 TYR cc_start: 0.7192 (m-80) cc_final: 0.6747 (m-80) outliers start: 103 outliers final: 86 residues processed: 324 average time/residue: 0.1551 time to fit residues: 80.4262 Evaluate side-chains 324 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 232 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain J residue 82 PHE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 301 ARG Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 66 ASN Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 269 MET Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 324 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 317 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 HIS ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.160812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112772 restraints weight = 55066.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109038 restraints weight = 44847.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109447 restraints weight = 45317.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109922 restraints weight = 42057.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110180 restraints weight = 36427.471| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29472 Z= 0.133 Angle : 0.531 14.187 40016 Z= 0.275 Chirality : 0.039 0.242 4484 Planarity : 0.003 0.038 5032 Dihedral : 4.729 51.218 4373 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 2.95 % Allowed : 17.77 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.14), residues: 3520 helix: 2.71 (0.23), residues: 460 sheet: 0.78 (0.15), residues: 1164 loop : -0.89 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 223 TYR 0.022 0.001 TYR K 62 PHE 0.016 0.001 PHE J 128 TRP 0.032 0.001 TRP J 24 HIS 0.006 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00312 (29384) covalent geometry : angle 0.52171 (39816) SS BOND : bond 0.00297 ( 64) SS BOND : angle 1.19643 ( 128) hydrogen bonds : bond 0.04571 ( 918) hydrogen bonds : angle 4.56064 ( 2652) link_BETA1-4 : bond 0.00697 ( 8) link_BETA1-4 : angle 1.39161 ( 24) link_NAG-ASN : bond 0.00098 ( 16) link_NAG-ASN : angle 2.21293 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 237 time to evaluate : 0.822 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: A 34 MET cc_start: 0.7085 (tmm) cc_final: 0.6799 (tpp) REVERT: A 77 ASP cc_start: 0.7774 (p0) cc_final: 0.7547 (p0) REVERT: A 88 LEU cc_start: 0.8434 (pt) cc_final: 0.8056 (mm) REVERT: A 157 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7444 (mp10) REVERT: A 167 MET cc_start: 0.8541 (mtp) cc_final: 0.8282 (ttm) REVERT: B 31 TYR cc_start: 0.7292 (m-80) cc_final: 0.7073 (m-80) REVERT: B 45 MET cc_start: 0.6365 (mmm) cc_final: 0.6119 (mmm) REVERT: B 157 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7956 (mtmm) REVERT: D 48 ARG cc_start: 0.7591 (mmp80) cc_final: 0.7045 (mmp80) REVERT: D 99 PHE cc_start: 0.8612 (p90) cc_final: 0.8382 (p90) REVERT: E 210 ASP cc_start: 0.8378 (t70) cc_final: 0.8159 (t70) REVERT: F 117 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.4539 (mm) REVERT: F 139 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6832 (ttm110) REVERT: F 250 ARG cc_start: 0.7297 (mmp-170) cc_final: 0.7024 (mmp-170) REVERT: J 82 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.5617 (m-80) REVERT: J 194 GLN cc_start: 0.7226 (tm-30) cc_final: 0.6601 (tm-30) REVERT: K 253 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8450 (tt) REVERT: M 120 MET cc_start: 0.7255 (mmp) cc_final: 0.6920 (mmp) REVERT: N 117 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7241 (mm) REVERT: N 166 GLN cc_start: 0.6275 (tp40) cc_final: 0.6035 (tp40) REVERT: N 223 TYR cc_start: 0.7160 (m-80) cc_final: 0.6724 (m-80) outliers start: 95 outliers final: 81 residues processed: 315 average time/residue: 0.1627 time to fit residues: 82.4377 Evaluate side-chains 316 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 228 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain J residue 82 PHE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 301 ARG Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 66 ASN Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 225 LEU Chi-restraints excluded: chain O residue 269 MET Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 100 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 165 optimal weight: 0.1980 chunk 275 optimal weight: 0.4980 chunk 190 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 260 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 319 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.160224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111726 restraints weight = 54880.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108030 restraints weight = 44897.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108654 restraints weight = 43865.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109334 restraints weight = 40054.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109341 restraints weight = 37301.980| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29472 Z= 0.149 Angle : 0.541 14.141 40016 Z= 0.280 Chirality : 0.039 0.237 4484 Planarity : 0.003 0.043 5032 Dihedral : 4.674 51.769 4369 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.68 % Rotamer: Outliers : 2.73 % Allowed : 18.02 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.14), residues: 3520 helix: 2.75 (0.23), residues: 460 sheet: 0.78 (0.15), residues: 1152 loop : -0.91 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 114 TYR 0.018 0.001 TYR K 62 PHE 0.015 0.001 PHE B 140 TRP 0.041 0.001 TRP J 24 HIS 0.008 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00350 (29384) covalent geometry : angle 0.53115 (39816) SS BOND : bond 0.00296 ( 64) SS BOND : angle 1.18822 ( 128) hydrogen bonds : bond 0.04684 ( 918) hydrogen bonds : angle 4.57440 ( 2652) link_BETA1-4 : bond 0.00654 ( 8) link_BETA1-4 : angle 1.38637 ( 24) link_NAG-ASN : bond 0.00115 ( 16) link_NAG-ASN : angle 2.29568 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7040 Ramachandran restraints generated. 3520 Oldfield, 0 Emsley, 3520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 225 time to evaluate : 0.895 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: A 34 MET cc_start: 0.7066 (tmm) cc_final: 0.6820 (tpp) REVERT: A 77 ASP cc_start: 0.7751 (p0) cc_final: 0.7540 (p0) REVERT: A 88 LEU cc_start: 0.8435 (pt) cc_final: 0.8074 (mm) REVERT: A 157 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7431 (mp10) REVERT: A 167 MET cc_start: 0.8510 (mtp) cc_final: 0.8281 (ttm) REVERT: B 31 TYR cc_start: 0.7221 (m-80) cc_final: 0.6998 (m-80) REVERT: B 45 MET cc_start: 0.6374 (mmm) cc_final: 0.6131 (mmm) REVERT: B 157 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8030 (mtmm) REVERT: D 48 ARG cc_start: 0.7633 (mmp80) cc_final: 0.7070 (mmp80) REVERT: E 210 ASP cc_start: 0.8359 (t70) cc_final: 0.8132 (t70) REVERT: F 117 LEU cc_start: 0.5013 (OUTLIER) cc_final: 0.4544 (mm) REVERT: F 139 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6843 (ttm110) REVERT: G 298 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8215 (mp) REVERT: J 82 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.5604 (m-80) REVERT: J 194 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6581 (tm-30) REVERT: K 253 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8451 (tt) REVERT: M 120 MET cc_start: 0.7380 (mmp) cc_final: 0.7042 (mmp) REVERT: N 117 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7101 (mm) REVERT: N 166 GLN cc_start: 0.6386 (tp40) cc_final: 0.6182 (tp40) REVERT: N 223 TYR cc_start: 0.7232 (m-80) cc_final: 0.6831 (m-80) outliers start: 88 outliers final: 79 residues processed: 298 average time/residue: 0.1603 time to fit residues: 77.0401 Evaluate side-chains 309 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 222 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 139 ARG Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain J residue 82 PHE Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 301 ARG Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 162 SER Chi-restraints excluded: chain K residue 168 THR Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 34 THR Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 66 ASN Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 225 LEU Chi-restraints excluded: chain O residue 269 MET Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 340 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 193 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 228 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.158291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108121 restraints weight = 55317.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107883 restraints weight = 42185.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107202 restraints weight = 37784.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.107453 restraints weight = 37423.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.107416 restraints weight = 35938.496| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29472 Z= 0.215 Angle : 0.602 14.099 40016 Z= 0.313 Chirality : 0.041 0.248 4484 Planarity : 0.004 0.040 5032 Dihedral : 4.973 54.857 4365 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 2.95 % Allowed : 17.80 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.14), residues: 3520 helix: 2.50 (0.24), residues: 460 sheet: 0.58 (0.16), residues: 1156 loop : -1.03 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 114 TYR 0.024 0.002 TYR I 215 PHE 0.027 0.002 PHE O 73 TRP 0.041 0.002 TRP J 24 HIS 0.011 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00513 (29384) covalent geometry : angle 0.59143 (39816) SS BOND : bond 0.00393 ( 64) SS BOND : angle 1.26950 ( 128) hydrogen bonds : bond 0.05392 ( 918) hydrogen bonds : angle 4.84612 ( 2652) link_BETA1-4 : bond 0.00579 ( 8) link_BETA1-4 : angle 1.32242 ( 24) link_NAG-ASN : bond 0.00259 ( 16) link_NAG-ASN : angle 2.62668 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4602.47 seconds wall clock time: 80 minutes 24.58 seconds (4824.58 seconds total)