Starting phenix.real_space_refine on Tue Jun 24 13:55:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrp_38609/06_2025/8xrp_38609.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrp_38609/06_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_38609/06_2025/8xrp_38609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrp_38609/06_2025/8xrp_38609.map" model { file = "/net/cci-nas-00/data/ceres_data/8xrp_38609/06_2025/8xrp_38609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrp_38609/06_2025/8xrp_38609.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.84, per 1000 atoms: 0.69 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: 7.79 Conformation dependent library (CDL) restraints added in 4.0 seconds 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: 4.78 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: 11.72 Time building geometry restraints manager: 9.31 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: 0.07 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: 112.070 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: 0.030 Extract box with map and model: 1.340 Check model and map are aligned: 0.210 Set scattering table: 0.300 Process input model: 71.940 Find NCS groups from input model: 1.370 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (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 TRP 0.028 0.002 TRP N 60 HIS 0.004 0.001 HIS N 266 PHE 0.027 0.002 PHE P 99 TYR 0.025 0.002 TYR J 268 ARG 0.005 0.001 ARG O 260 Details of bonding type rmsd link_NAG-ASN : bond 0.01173 ( 16) link_NAG-ASN : angle 4.30537 ( 48) link_BETA1-4 : bond 0.01272 ( 8) link_BETA1-4 : angle 2.26920 ( 24) hydrogen bonds : bond 0.21044 ( 918) hydrogen bonds : angle 8.71370 ( 2652) SS BOND : bond 0.05447 ( 64) SS BOND : angle 5.53959 ( 128) covalent geometry : bond 0.01296 (29384) covalent geometry : angle 1.59113 (39816) *********************** 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 : 3.253 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: 0.4264 time to fit residues: 445.7972 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 : 3.414 ------------------------------------------------------------------------------- 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 297 optimal weight: 7.9990 chunk 266 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 205 optimal weight: 0.3980 chunk 319 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN C 268 ASN D 102 GLN E 50 ASN F 87 GLN F 120 GLN G 134 GLN G 255 ASN G 268 ASN H 102 GLN I 42 GLN I 57 GLN I 152 GLN J 87 GLN J 248 ASN ** 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.177933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.150414 restraints weight = 58978.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.153040 restraints weight = 138713.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.152680 restraints weight = 55263.715| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29472 Z= 0.155 Angle : 0.639 10.160 40016 Z= 0.335 Chirality : 0.043 0.263 4484 Planarity : 0.004 0.059 5032 Dihedral : 7.623 63.117 4382 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.26 % Allowed : 15.26 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3520 helix: 3.20 (0.22), residues: 472 sheet: 1.01 (0.15), residues: 1224 loop : -0.65 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 228 HIS 0.013 0.001 HIS B 91 PHE 0.021 0.002 PHE O 60 TYR 0.024 0.002 TYR J 314 ARG 0.007 0.001 ARG E 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 16) link_NAG-ASN : angle 2.96017 ( 48) link_BETA1-4 : bond 0.01026 ( 8) link_BETA1-4 : angle 2.10306 ( 24) hydrogen bonds : bond 0.05962 ( 918) hydrogen bonds : angle 5.78002 ( 2652) SS BOND : bond 0.00384 ( 64) SS BOND : angle 1.72085 ( 128) covalent geometry : bond 0.00346 (29384) covalent geometry : angle 0.62214 (39816) *********************** 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 395 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 322 time to evaluate : 3.273 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: A 34 MET cc_start: 0.7087 (tmm) cc_final: 0.6591 (tpp) REVERT: A 88 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8073 (mm) REVERT: A 157 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6784 (mp10) REVERT: A 210 ASP cc_start: 0.8607 (t0) cc_final: 0.7950 (t0) REVERT: B 240 ASN cc_start: 0.7606 (t0) cc_final: 0.7365 (t0) REVERT: F 194 GLN cc_start: 0.6799 (tm-30) cc_final: 0.6526 (tm-30) REVERT: G 259 TYR cc_start: 0.5523 (p90) cc_final: 0.5188 (p90) REVERT: I 73 ASP cc_start: 0.7714 (t70) cc_final: 0.7390 (t0) REVERT: J 87 GLN cc_start: 0.2072 (OUTLIER) cc_final: 0.1681 (mt0) REVERT: J 104 LEU cc_start: 0.6331 (mt) cc_final: 0.5963 (tt) REVERT: J 194 GLN cc_start: 0.7329 (tm-30) cc_final: 0.7051 (tm-30) REVERT: M 88 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7140 (mm) REVERT: M 164 ASP cc_start: 0.8223 (t0) cc_final: 0.7988 (t0) outliers start: 73 outliers final: 37 residues processed: 381 average time/residue: 0.5224 time to fit residues: 317.9851 Evaluate side-chains 305 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 7.964 ------------------------------------------------------------------------------- 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 146 THR Chi-restraints excluded: chain B residue 180 VAL 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 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 129 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain G residue 33 VAL 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 J residue 87 GLN 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 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain N residue 31 TYR 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 53 LEU Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 217 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 325 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 256 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 250 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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** F 87 GLN I 57 GLN ** 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 166 GLN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.178014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.146314 restraints weight = 59172.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.143291 restraints weight = 85003.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.144998 restraints weight = 81657.813| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29472 Z= 0.116 Angle : 0.558 10.394 40016 Z= 0.290 Chirality : 0.040 0.254 4484 Planarity : 0.003 0.038 5032 Dihedral : 5.780 53.915 4372 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.67 % Allowed : 15.45 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3520 helix: 3.10 (0.22), residues: 472 sheet: 0.99 (0.15), residues: 1228 loop : -0.69 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP J 24 HIS 0.007 0.001 HIS F 105 PHE 0.021 0.001 PHE E 118 TYR 0.018 0.001 TYR J 220 ARG 0.005 0.000 ARG E 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 16) link_NAG-ASN : angle 2.52031 ( 48) link_BETA1-4 : bond 0.00907 ( 8) link_BETA1-4 : angle 1.66205 ( 24) hydrogen bonds : bond 0.05054 ( 918) hydrogen bonds : angle 5.09628 ( 2652) SS BOND : bond 0.00255 ( 64) SS BOND : angle 1.60341 ( 128) covalent geometry : bond 0.00254 (29384) covalent geometry : angle 0.54364 (39816) *********************** 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 383 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 297 time to evaluate : 4.284 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: 0.7381 (tmm) cc_final: 0.6873 (tpp) REVERT: A 88 LEU cc_start: 0.8331 (pt) cc_final: 0.7967 (mm) REVERT: A 157 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6716 (mp10) REVERT: A 210 ASP cc_start: 0.8611 (t0) cc_final: 0.8050 (t0) REVERT: C 137 GLU cc_start: 0.6665 (pt0) cc_final: 0.6159 (pt0) REVERT: D 64 TRP cc_start: 0.3709 (p90) cc_final: 0.3502 (p90) REVERT: D 124 GLU cc_start: 0.5984 (mp0) cc_final: 0.5552 (mp0) REVERT: E 210 ASP cc_start: 0.7790 (t0) cc_final: 0.7542 (t0) REVERT: I 73 ASP cc_start: 0.7774 (t70) cc_final: 0.7505 (t0) REVERT: J 104 LEU cc_start: 0.6388 (mt) cc_final: 0.5868 (tt) REVERT: J 194 GLN cc_start: 0.7400 (tm-30) cc_final: 0.6929 (tm-30) REVERT: K 137 GLU cc_start: 0.6435 (mp0) cc_final: 0.6221 (pm20) REVERT: M 88 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6895 (mm) REVERT: N 117 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7576 (mm) outliers start: 86 outliers final: 43 residues processed: 360 average time/residue: 0.5434 time to fit residues: 313.7216 Evaluate side-chains 303 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 5.332 ------------------------------------------------------------------------------- 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 109 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 53 LEU 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 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 216 LEU Chi-restraints excluded: chain F residue 129 LEU 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 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 101 LEU Chi-restraints excluded: chain J residue 213 ASP 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 167 LEU Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 216 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 270 SER Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain O residue 60 PHE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 209 SER Chi-restraints excluded: chain O residue 276 LYS Chi-restraints excluded: chain O residue 290 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 61 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 322 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 166 GLN K 61 HIS ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN M 53 GLN M 57 GLN M 168 GLN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN N 311 GLN O 134 GLN ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.162851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126278 restraints weight = 55468.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.118894 restraints weight = 84590.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115881 restraints weight = 72256.677| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 29472 Z= 0.275 Angle : 0.694 9.797 40016 Z= 0.363 Chirality : 0.044 0.293 4484 Planarity : 0.005 0.079 5032 Dihedral : 5.508 45.827 4372 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 3.69 % Allowed : 15.51 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3520 helix: 2.38 (0.23), residues: 460 sheet: 0.82 (0.15), residues: 1224 loop : -0.83 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP O 228 HIS 0.009 0.001 HIS B 216 PHE 0.030 0.003 PHE O 73 TYR 0.030 0.002 TYR D 36 ARG 0.007 0.001 ARG D 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 16) link_NAG-ASN : angle 3.03701 ( 48) link_BETA1-4 : bond 0.00771 ( 8) link_BETA1-4 : angle 1.55660 ( 24) hydrogen bonds : bond 0.06160 ( 918) hydrogen bonds : angle 5.33107 ( 2652) SS BOND : bond 0.00414 ( 64) SS BOND : angle 1.76265 ( 128) covalent geometry : bond 0.00664 (29384) covalent geometry : angle 0.67926 (39816) *********************** 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: 119 poor density : 277 time to evaluate : 3.592 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: 0.7477 (tmm) cc_final: 0.6876 (tpp) REVERT: A 157 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: A 164 ASP cc_start: 0.8253 (t0) cc_final: 0.7973 (m-30) REVERT: A 210 ASP cc_start: 0.8468 (t0) cc_final: 0.8064 (t0) REVERT: E 210 ASP cc_start: 0.8197 (t0) cc_final: 0.7838 (t0) REVERT: F 117 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.4898 (mm) REVERT: G 190 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7232 (tp30) REVERT: J 194 GLN cc_start: 0.7446 (tm-30) cc_final: 0.6777 (tm-30) REVERT: M 120 MET cc_start: 0.7401 (mmp) cc_final: 0.6965 (mmp) REVERT: N 166 GLN cc_start: 0.5939 (tp-100) cc_final: 0.5653 (tp40) outliers start: 119 outliers final: 64 residues processed: 374 average time/residue: 0.4082 time to fit residues: 241.6636 Evaluate side-chains 310 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 243 time to evaluate : 3.188 ------------------------------------------------------------------------------- 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 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 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 D residue 62 CYS Chi-restraints excluded: chain D residue 76 PHE 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 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 299 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 33 VAL 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 I residue 65 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 212 VAL 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 J residue 277 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 N residue 26 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 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 197 THR 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 319 optimal weight: 0.5980 chunk 225 optimal weight: 0.1980 chunk 307 optimal weight: 3.9990 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 chunk 314 optimal weight: 3.9990 chunk 257 optimal weight: 40.0000 chunk 262 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN N 105 HIS ** 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 = 0.4250 r_free = 0.4250 target = 0.165513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.131140 restraints weight = 54758.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.120757 restraints weight = 72996.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119855 restraints weight = 74950.647| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 29472 Z= 0.108 Angle : 0.538 11.571 40016 Z= 0.280 Chirality : 0.039 0.240 4484 Planarity : 0.003 0.039 5032 Dihedral : 4.882 41.668 4372 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.05 % Allowed : 16.94 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3520 helix: 2.87 (0.23), residues: 472 sheet: 1.02 (0.15), residues: 1204 loop : -0.84 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 24 HIS 0.007 0.001 HIS F 105 PHE 0.019 0.001 PHE J 128 TYR 0.022 0.001 TYR G 71 ARG 0.008 0.000 ARG D 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 16) link_NAG-ASN : angle 2.33599 ( 48) link_BETA1-4 : bond 0.00887 ( 8) link_BETA1-4 : angle 1.49946 ( 24) hydrogen bonds : bond 0.04643 ( 918) hydrogen bonds : angle 4.76863 ( 2652) SS BOND : bond 0.00351 ( 64) SS BOND : angle 1.50533 ( 128) covalent geometry : bond 0.00240 (29384) covalent geometry : angle 0.52496 (39816) *********************** 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 332 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 266 time to evaluate : 3.684 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: 0.7356 (tmm) cc_final: 0.6858 (tpp) REVERT: A 157 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: A 210 ASP cc_start: 0.8653 (t0) cc_final: 0.8257 (t0) REVERT: E 210 ASP cc_start: 0.8131 (t0) cc_final: 0.7808 (t0) REVERT: F 26 LEU cc_start: 0.5805 (tt) cc_final: 0.5224 (tp) REVERT: G 253 LEU cc_start: 0.8121 (mm) cc_final: 0.7475 (tp) REVERT: G 269 MET cc_start: 0.6127 (pmm) cc_final: 0.5709 (pmm) REVERT: J 194 GLN cc_start: 0.7471 (tm-30) cc_final: 0.6746 (tm-30) REVERT: M 120 MET cc_start: 0.7187 (mmp) cc_final: 0.6812 (mmp) REVERT: M 175 GLU cc_start: 0.7244 (tp30) cc_final: 0.7020 (tp30) REVERT: N 117 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7581 (mm) outliers start: 66 outliers final: 46 residues processed: 314 average time/residue: 0.4220 time to fit residues: 210.1957 Evaluate side-chains 288 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 3.392 ------------------------------------------------------------------------------- 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 89 THR Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 THR 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 140 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 216 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 G residue 71 TYR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 140 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 133 MET 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 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain N residue 26 LEU 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 O residue 96 THR Chi-restraints excluded: chain O residue 129 ASN 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 50 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 339 optimal weight: 4.9990 chunk 309 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN G 66 ASN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 GLN M 168 GLN ** 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 = 0.4192 r_free = 0.4192 target = 0.160495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112043 restraints weight = 55840.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.107772 restraints weight = 49242.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108138 restraints weight = 48995.909| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 29472 Z= 0.207 Angle : 0.601 13.931 40016 Z= 0.313 Chirality : 0.041 0.296 4484 Planarity : 0.004 0.049 5032 Dihedral : 4.972 35.703 4372 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.85 % Allowed : 16.63 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3520 helix: 2.63 (0.24), residues: 460 sheet: 0.79 (0.15), residues: 1216 loop : -0.84 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 24 HIS 0.007 0.001 HIS F 105 PHE 0.022 0.002 PHE B 228 TYR 0.019 0.002 TYR I 215 ARG 0.013 0.001 ARG G 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 16) link_NAG-ASN : angle 2.63916 ( 48) link_BETA1-4 : bond 0.00665 ( 8) link_BETA1-4 : angle 1.42432 ( 24) hydrogen bonds : bond 0.05339 ( 918) hydrogen bonds : angle 4.91694 ( 2652) SS BOND : bond 0.00333 ( 64) SS BOND : angle 1.50173 ( 128) covalent geometry : bond 0.00495 (29384) covalent geometry : angle 0.58795 (39816) *********************** 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 342 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 250 time to evaluate : 3.614 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: 0.7447 (tmm) cc_final: 0.7030 (tpp) REVERT: A 88 LEU cc_start: 0.8455 (pt) cc_final: 0.8010 (mm) REVERT: A 157 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: A 210 ASP cc_start: 0.8479 (t0) cc_final: 0.8108 (t0) REVERT: D 58 ASP cc_start: 0.7993 (t0) cc_final: 0.7762 (t0) REVERT: D 98 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7422 (mm-40) REVERT: E 38 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8230 (tp) REVERT: E 210 ASP cc_start: 0.8359 (t0) cc_final: 0.7915 (t0) REVERT: F 117 LEU cc_start: 0.5256 (OUTLIER) cc_final: 0.4857 (mt) REVERT: G 253 LEU cc_start: 0.8324 (mm) cc_final: 0.7551 (tp) REVERT: G 259 TYR cc_start: 0.7077 (p90) cc_final: 0.6529 (p90) REVERT: G 269 MET cc_start: 0.6112 (pmm) cc_final: 0.5617 (pmm) REVERT: J 194 GLN cc_start: 0.7280 (tm-30) cc_final: 0.6505 (tm-30) REVERT: M 120 MET cc_start: 0.7228 (mmp) cc_final: 0.6787 (mmp) REVERT: N 117 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7400 (mm) REVERT: O 100 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.9132 (m) outliers start: 92 outliers final: 67 residues processed: 319 average time/residue: 0.3983 time to fit residues: 202.8480 Evaluate side-chains 309 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 236 time to evaluate : 3.285 ------------------------------------------------------------------------------- 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 79 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 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 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 62 CYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 98 GLN 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 38 LEU 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 F residue 307 SER Chi-restraints excluded: chain G residue 61 HIS 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 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 212 VAL 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 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 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 250 ARG Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 66 ASN Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 100 VAL 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 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 236 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 chunk 198 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** G 66 ASN K 81 HIS ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN N 166 GLN ** 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 = 0.4217 r_free = 0.4217 target = 0.162324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.114253 restraints weight = 55390.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110271 restraints weight = 49210.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111346 restraints weight = 44962.852| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29472 Z= 0.117 Angle : 0.529 12.014 40016 Z= 0.275 Chirality : 0.039 0.241 4484 Planarity : 0.003 0.041 5032 Dihedral : 4.694 36.513 4372 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.14 % Allowed : 17.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3520 helix: 2.82 (0.23), residues: 460 sheet: 0.82 (0.15), residues: 1236 loop : -0.81 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 60 HIS 0.008 0.001 HIS F 105 PHE 0.018 0.001 PHE N 128 TYR 0.017 0.001 TYR J 220 ARG 0.009 0.000 ARG D 48 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 16) link_NAG-ASN : angle 2.26116 ( 48) link_BETA1-4 : bond 0.00758 ( 8) link_BETA1-4 : angle 1.41929 ( 24) hydrogen bonds : bond 0.04600 ( 918) hydrogen bonds : angle 4.61914 ( 2652) SS BOND : bond 0.00286 ( 64) SS BOND : angle 1.33817 ( 128) covalent geometry : bond 0.00266 (29384) covalent geometry : angle 0.51752 (39816) *********************** 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 312 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 243 time to evaluate : 3.226 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: 0.7285 (tmm) cc_final: 0.6942 (tpp) REVERT: A 88 LEU cc_start: 0.8422 (pt) cc_final: 0.7955 (mm) REVERT: A 157 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: D 58 ASP cc_start: 0.7988 (t0) cc_final: 0.7780 (t0) REVERT: D 98 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7477 (mm-40) REVERT: E 210 ASP cc_start: 0.8318 (t0) cc_final: 0.7899 (t0) REVERT: F 117 LEU cc_start: 0.5225 (OUTLIER) cc_final: 0.4810 (mt) REVERT: G 253 LEU cc_start: 0.8264 (mm) cc_final: 0.7527 (tp) REVERT: G 259 TYR cc_start: 0.7117 (p90) cc_final: 0.6533 (p90) REVERT: G 269 MET cc_start: 0.6168 (pmm) cc_final: 0.5634 (pmm) REVERT: J 194 GLN cc_start: 0.7296 (tm-30) cc_final: 0.6551 (tm-30) REVERT: M 120 MET cc_start: 0.7165 (mmp) cc_final: 0.6737 (mmp) REVERT: N 117 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7360 (mm) REVERT: O 100 VAL cc_start: 0.9346 (OUTLIER) cc_final: 0.9106 (m) outliers start: 69 outliers final: 56 residues processed: 293 average time/residue: 0.4132 time to fit residues: 192.6640 Evaluate side-chains 295 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 3.202 ------------------------------------------------------------------------------- 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 A residue 164 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 32 ASP 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 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 108 LEU 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 71 TYR Chi-restraints excluded: chain G residue 96 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 82 VAL Chi-restraints excluded: chain I residue 133 MET 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 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 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 117 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 129 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 133 optimal weight: 9.9990 chunk 327 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 349 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 321 optimal weight: 0.6980 chunk 204 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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** E 157 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN N 166 GLN ** 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 = 0.4182 r_free = 0.4182 target = 0.159642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112685 restraints weight = 55922.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109441 restraints weight = 61410.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110469 restraints weight = 55239.294| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 29472 Z= 0.220 Angle : 0.600 15.087 40016 Z= 0.313 Chirality : 0.041 0.256 4484 Planarity : 0.004 0.043 5032 Dihedral : 4.932 35.311 4372 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.64 % Allowed : 17.12 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3520 helix: 2.56 (0.24), residues: 460 sheet: 0.71 (0.15), residues: 1212 loop : -0.91 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 60 HIS 0.006 0.001 HIS F 105 PHE 0.024 0.002 PHE O 73 TYR 0.021 0.002 TYR I 215 ARG 0.013 0.001 ARG D 48 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 16) link_NAG-ASN : angle 2.59694 ( 48) link_BETA1-4 : bond 0.00635 ( 8) link_BETA1-4 : angle 1.40185 ( 24) hydrogen bonds : bond 0.05360 ( 918) hydrogen bonds : angle 4.84374 ( 2652) SS BOND : bond 0.00548 ( 64) SS BOND : angle 1.47567 ( 128) covalent geometry : bond 0.00522 (29384) covalent geometry : angle 0.58779 (39816) *********************** 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 320 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 235 time to evaluate : 3.687 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: 0.7464 (tmm) cc_final: 0.7081 (tpp) REVERT: A 88 LEU cc_start: 0.8417 (pt) cc_final: 0.8060 (mm) REVERT: A 157 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7438 (mp10) REVERT: E 210 ASP cc_start: 0.8365 (t0) cc_final: 0.7956 (t0) REVERT: F 117 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.5095 (mt) REVERT: G 259 TYR cc_start: 0.6896 (p90) cc_final: 0.6460 (p90) REVERT: G 269 MET cc_start: 0.6383 (pmm) cc_final: 0.5805 (pmm) REVERT: J 194 GLN cc_start: 0.7461 (tm-30) cc_final: 0.6667 (tm-30) REVERT: M 120 MET cc_start: 0.7331 (mmp) cc_final: 0.6883 (mmp) REVERT: N 117 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7581 (mm) REVERT: O 100 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9144 (m) outliers start: 85 outliers final: 66 residues processed: 302 average time/residue: 0.4002 time to fit residues: 192.6129 Evaluate side-chains 294 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 224 time to evaluate : 3.453 ------------------------------------------------------------------------------- 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 A residue 164 ASP 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 146 THR 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 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 62 CYS Chi-restraints excluded: chain D residue 76 PHE 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 306 ILE Chi-restraints excluded: chain F residue 307 SER 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 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 I residue 168 GLN Chi-restraints excluded: chain I residue 212 VAL 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 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 276 LYS Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 74 THR 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 250 ARG Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain O residue 66 ASN Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 100 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 102 optimal weight: 0.9980 chunk 279 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 320 optimal weight: 0.3980 chunk 115 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 345 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** E 157 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN N 166 GLN ** 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 = 0.4211 r_free = 0.4211 target = 0.161984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113321 restraints weight = 55304.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109754 restraints weight = 45714.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110764 restraints weight = 42131.060| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29472 Z= 0.117 Angle : 0.526 14.472 40016 Z= 0.273 Chirality : 0.039 0.240 4484 Planarity : 0.003 0.038 5032 Dihedral : 4.635 36.838 4372 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.20 % Allowed : 17.74 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3520 helix: 2.80 (0.23), residues: 460 sheet: 0.79 (0.15), residues: 1200 loop : -0.84 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F 24 HIS 0.007 0.001 HIS F 105 PHE 0.014 0.001 PHE N 128 TYR 0.022 0.001 TYR O 71 ARG 0.014 0.000 ARG D 48 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 16) link_NAG-ASN : angle 2.15671 ( 48) link_BETA1-4 : bond 0.00756 ( 8) link_BETA1-4 : angle 1.42520 ( 24) hydrogen bonds : bond 0.04485 ( 918) hydrogen bonds : angle 4.51853 ( 2652) SS BOND : bond 0.00468 ( 64) SS BOND : angle 1.19144 ( 128) covalent geometry : bond 0.00270 (29384) covalent geometry : angle 0.51688 (39816) *********************** 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 306 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 235 time to evaluate : 3.224 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: 0.7187 (tmm) cc_final: 0.6927 (tpp) REVERT: A 88 LEU cc_start: 0.8408 (pt) cc_final: 0.8046 (mm) REVERT: A 120 MET cc_start: 0.8519 (mmp) cc_final: 0.8197 (mmp) REVERT: A 157 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: A 167 MET cc_start: 0.8525 (mtp) cc_final: 0.8279 (ttm) REVERT: B 31 TYR cc_start: 0.7304 (m-80) cc_final: 0.7070 (m-80) REVERT: B 157 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8128 (mtmm) REVERT: D 58 ASP cc_start: 0.8066 (t0) cc_final: 0.7423 (t0) REVERT: E 210 ASP cc_start: 0.8378 (t0) cc_final: 0.7954 (t0) REVERT: F 78 GLN cc_start: 0.6497 (mt0) cc_final: 0.6000 (mm-40) REVERT: F 117 LEU cc_start: 0.5152 (OUTLIER) cc_final: 0.4758 (mt) REVERT: G 259 TYR cc_start: 0.7129 (p90) cc_final: 0.6859 (p90) REVERT: G 269 MET cc_start: 0.6224 (pmm) cc_final: 0.5777 (pmm) REVERT: J 194 GLN cc_start: 0.7283 (tm-30) cc_final: 0.6616 (tm-30) REVERT: M 120 MET cc_start: 0.7233 (mmp) cc_final: 0.6851 (mmp) REVERT: N 117 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7197 (mm) REVERT: N 166 GLN cc_start: 0.5845 (tp-100) cc_final: 0.5615 (tp40) REVERT: O 100 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9098 (m) outliers start: 71 outliers final: 58 residues processed: 289 average time/residue: 0.4670 time to fit residues: 215.6093 Evaluate side-chains 290 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 227 time to evaluate : 4.327 ------------------------------------------------------------------------------- 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 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 146 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 291 THR 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 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 76 PHE 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 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 174 THR Chi-restraints excluded: chain F residue 307 SER 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 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 I residue 212 VAL 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 K residue 33 VAL Chi-restraints excluded: chain K residue 96 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 50 CYS Chi-restraints excluded: chain N residue 74 THR 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 O residue 96 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 197 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 268 optimal weight: 0.6980 chunk 291 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 320 optimal weight: 0.0470 chunk 208 optimal weight: 0.6980 chunk 347 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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** E 157 GLN F 166 GLN I 152 GLN I 179 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** 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 = 0.4220 r_free = 0.4220 target = 0.162539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114902 restraints weight = 55449.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110748 restraints weight = 51391.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111749 restraints weight = 46857.981| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 29472 Z= 0.104 Angle : 0.516 14.315 40016 Z= 0.266 Chirality : 0.038 0.239 4484 Planarity : 0.003 0.036 5032 Dihedral : 4.443 37.083 4372 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.89 % Allowed : 17.77 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3520 helix: 2.98 (0.24), residues: 460 sheet: 0.86 (0.15), residues: 1228 loop : -0.84 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP F 24 HIS 0.007 0.001 HIS F 105 PHE 0.013 0.001 PHE N 128 TYR 0.020 0.001 TYR F 220 ARG 0.009 0.000 ARG F 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 16) link_NAG-ASN : angle 2.06563 ( 48) link_BETA1-4 : bond 0.00735 ( 8) link_BETA1-4 : angle 1.44332 ( 24) hydrogen bonds : bond 0.04171 ( 918) hydrogen bonds : angle 4.35953 ( 2652) SS BOND : bond 0.00360 ( 64) SS BOND : angle 1.12634 ( 128) covalent geometry : bond 0.00237 (29384) covalent geometry : angle 0.50672 (39816) ********************** 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 296 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 4.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7222 (tmm) cc_final: 0.7006 (tpp) REVERT: A 88 LEU cc_start: 0.8427 (pt) cc_final: 0.8029 (mm) REVERT: A 120 MET cc_start: 0.8410 (mmp) cc_final: 0.8094 (mmp) REVERT: A 157 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: A 167 MET cc_start: 0.8539 (mtp) cc_final: 0.8299 (ttm) REVERT: B 31 TYR cc_start: 0.7198 (m-80) cc_final: 0.6948 (m-80) REVERT: B 45 MET cc_start: 0.6242 (mmm) cc_final: 0.5970 (mmm) REVERT: B 157 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7914 (mtmm) REVERT: E 120 MET cc_start: 0.7173 (mmp) cc_final: 0.6701 (mmp) REVERT: E 210 ASP cc_start: 0.8362 (t0) cc_final: 0.7950 (t0) REVERT: F 78 GLN cc_start: 0.6454 (mt0) cc_final: 0.6032 (mm-40) REVERT: F 117 LEU cc_start: 0.5132 (OUTLIER) cc_final: 0.4731 (mt) REVERT: G 259 TYR cc_start: 0.7054 (p90) cc_final: 0.6809 (p90) REVERT: G 269 MET cc_start: 0.6288 (pmm) cc_final: 0.5808 (pmm) REVERT: G 271 ASN cc_start: 0.7017 (p0) cc_final: 0.6594 (p0) REVERT: J 194 GLN cc_start: 0.7254 (tm-30) cc_final: 0.6706 (tm-30) REVERT: M 120 MET cc_start: 0.7091 (mmp) cc_final: 0.6733 (mmp) REVERT: N 31 TYR cc_start: 0.6021 (m-80) cc_final: 0.5524 (m-80) REVERT: N 117 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7241 (mm) REVERT: O 100 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.9103 (m) outliers start: 61 outliers final: 52 residues processed: 284 average time/residue: 0.4398 time to fit residues: 200.7715 Evaluate side-chains 280 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 3.356 ------------------------------------------------------------------------------- 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 79 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 291 THR 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 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 VAL 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 174 THR Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 96 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 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 212 VAL 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 307 SER Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR 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 74 THR 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 O residue 96 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 129 ASN Chi-restraints excluded: chain O residue 197 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 300 optimal weight: 2.9990 chunk 303 optimal weight: 0.0270 chunk 329 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 305 optimal weight: 2.9990 chunk 347 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 271 optimal weight: 0.8980 overall best weight: 1.5442 ------------------------------------------------------------------------------- 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** E 50 ASN E 157 GLN I 179 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 GLN ** N 87 GLN ** 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 = 0.4194 r_free = 0.4194 target = 0.160586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111591 restraints weight = 55361.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.107996 restraints weight = 45461.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108795 restraints weight = 42758.789| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29472 Z= 0.163 Angle : 0.561 14.056 40016 Z= 0.290 Chirality : 0.040 0.243 4484 Planarity : 0.004 0.037 5032 Dihedral : 4.598 40.483 4364 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 1.99 % Allowed : 17.87 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3520 helix: 2.80 (0.24), residues: 460 sheet: 0.82 (0.15), residues: 1200 loop : -0.85 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP F 24 HIS 0.009 0.001 HIS F 105 PHE 0.021 0.002 PHE O 73 TYR 0.026 0.001 TYR I 215 ARG 0.010 0.000 ARG E 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 16) link_NAG-ASN : angle 2.51590 ( 48) link_BETA1-4 : bond 0.00699 ( 8) link_BETA1-4 : angle 1.47794 ( 24) hydrogen bonds : bond 0.04797 ( 918) hydrogen bonds : angle 4.55402 ( 2652) SS BOND : bond 0.00336 ( 64) SS BOND : angle 1.21509 ( 128) covalent geometry : bond 0.00389 (29384) covalent geometry : angle 0.55044 (39816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10988.25 seconds wall clock time: 197 minutes 57.97 seconds (11877.97 seconds total)