Starting phenix.real_space_refine on Mon May 26 16:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrp_38609/05_2025/8xrp_38609.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrp_38609/05_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_38609/05_2025/8xrp_38609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrp_38609/05_2025/8xrp_38609.map" model { file = "/net/cci-nas-00/data/ceres_data/8xrp_38609/05_2025/8xrp_38609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrp_38609/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 16.85, per 1000 atoms: 0.59 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: 6.83 Conformation dependent library (CDL) restraints added in 3.5 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: 4.98 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: 11.07 Time building geometry restraints manager: 7.80 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: 7.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.180 Check model and map are aligned: 0.190 Set scattering table: 0.300 Process input model: 63.670 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.880 ------------------------------------------------------------------------------- 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 : 3.011 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: 0.4383 time to fit residues: 458.1903 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 : 3.429 ------------------------------------------------------------------------------- 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 = 58978.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.153039 restraints weight = 138717.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.152680 restraints weight = 55268.094| |-----------------------------------------------------------------------------| 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 : 3.013 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: 0.7088 (tmm) cc_final: 0.6592 (tpp) REVERT: A 88 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8072 (mm) REVERT: A 157 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6785 (mp10) REVERT: A 210 ASP cc_start: 0.8607 (t0) cc_final: 0.7950 (t0) REVERT: B 240 ASN cc_start: 0.7607 (t0) cc_final: 0.7365 (t0) REVERT: F 194 GLN cc_start: 0.6798 (tm-30) cc_final: 0.6525 (tm-30) REVERT: G 259 TYR cc_start: 0.5525 (p90) cc_final: 0.5189 (p90) REVERT: I 73 ASP cc_start: 0.7714 (t70) cc_final: 0.7391 (t0) REVERT: J 87 GLN cc_start: 0.2073 (OUTLIER) cc_final: 0.1682 (mt0) REVERT: J 104 LEU cc_start: 0.6331 (mt) cc_final: 0.5963 (tt) REVERT: J 194 GLN cc_start: 0.7328 (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: 0.8224 (t0) cc_final: 0.7989 (t0) outliers start: 73 outliers final: 37 residues processed: 381 average time/residue: 0.3825 time to fit residues: 231.9430 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 : 3.014 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 325 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 250 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 105 HIS ** 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 = 0.4433 r_free = 0.4433 target = 0.176463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.144237 restraints weight = 58782.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.141525 restraints weight = 89256.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.143317 restraints weight = 84553.079| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29472 Z= 0.136 Angle : 0.576 10.220 40016 Z= 0.300 Chirality : 0.041 0.256 4484 Planarity : 0.004 0.038 5032 Dihedral : 5.680 53.377 4372 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.92 % Allowed : 15.11 % Favored : 81.98 % 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: 0.62 (0.14), residues: 3520 helix: 3.01 (0.22), residues: 472 sheet: 0.95 (0.15), residues: 1244 loop : -0.71 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP J 24 HIS 0.008 0.001 HIS F 105 PHE 0.022 0.002 PHE E 118 TYR 0.020 0.002 TYR J 220 ARG 0.006 0.000 ARG E 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 16) link_NAG-ASN : angle 2.58285 ( 48) link_BETA1-4 : bond 0.00803 ( 8) link_BETA1-4 : angle 1.60037 ( 24) hydrogen bonds : bond 0.05220 ( 918) hydrogen bonds : angle 5.09627 ( 2652) SS BOND : bond 0.00305 ( 64) SS BOND : angle 1.60844 ( 128) covalent geometry : bond 0.00311 (29384) covalent geometry : angle 0.56197 (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 392 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 298 time to evaluate : 3.071 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: A 34 MET cc_start: 0.7333 (tmm) cc_final: 0.6864 (tpp) REVERT: A 88 LEU cc_start: 0.8357 (pt) cc_final: 0.7984 (mm) REVERT: A 157 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6871 (mp10) REVERT: A 210 ASP cc_start: 0.8623 (t0) cc_final: 0.8075 (t0) REVERT: C 137 GLU cc_start: 0.6675 (pt0) cc_final: 0.6207 (pt0) REVERT: E 210 ASP cc_start: 0.7831 (t0) cc_final: 0.7620 (t0) REVERT: F 194 GLN cc_start: 0.6834 (tm-30) cc_final: 0.5963 (tm-30) REVERT: I 73 ASP cc_start: 0.7789 (t70) cc_final: 0.7521 (t0) REVERT: J 104 LEU cc_start: 0.6291 (mt) cc_final: 0.5839 (tt) REVERT: J 194 GLN cc_start: 0.7440 (tm-30) cc_final: 0.6978 (tm-30) REVERT: M 88 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6982 (mm) REVERT: N 117 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7640 (mm) outliers start: 94 outliers final: 47 residues processed: 367 average time/residue: 0.3986 time to fit residues: 229.9515 Evaluate side-chains 302 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 3.054 ------------------------------------------------------------------------------- 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 191 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 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 65 THR 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 270 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 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: 1.9990 chunk 165 optimal weight: 10.0000 chunk 259 optimal weight: 30.0000 chunk 78 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 322 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 138 GLN M 168 GLN ** N 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN N 311 GLN O 134 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.162596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.127470 restraints weight = 55273.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117689 restraints weight = 76181.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115074 restraints weight = 79347.336| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 29472 Z= 0.249 Angle : 0.669 9.218 40016 Z= 0.351 Chirality : 0.043 0.312 4484 Planarity : 0.005 0.067 5032 Dihedral : 5.352 44.357 4372 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 3.44 % Allowed : 15.94 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.46 (0.23), residues: 460 sheet: 0.82 (0.15), residues: 1240 loop : -0.87 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 60 HIS 0.008 0.001 HIS B 216 PHE 0.027 0.003 PHE C 73 TYR 0.023 0.002 TYR J 268 ARG 0.010 0.001 ARG D 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 16) link_NAG-ASN : angle 2.92258 ( 48) link_BETA1-4 : bond 0.00589 ( 8) link_BETA1-4 : angle 1.47619 ( 24) hydrogen bonds : bond 0.05895 ( 918) hydrogen bonds : angle 5.20473 ( 2652) SS BOND : bond 0.00521 ( 64) SS BOND : angle 1.80697 ( 128) covalent geometry : bond 0.00594 (29384) covalent geometry : angle 0.65425 (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 379 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 268 time to evaluate : 3.642 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: 0.7432 (tmm) cc_final: 0.6983 (tpp) REVERT: A 157 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: A 210 ASP cc_start: 0.8518 (t0) cc_final: 0.8110 (t0) REVERT: E 210 ASP cc_start: 0.8209 (t0) cc_final: 0.7866 (t0) REVERT: F 117 LEU cc_start: 0.5602 (OUTLIER) cc_final: 0.5018 (mm) REVERT: F 194 GLN cc_start: 0.6718 (tm-30) cc_final: 0.6046 (tm-30) REVERT: J 194 GLN cc_start: 0.7496 (tm-30) cc_final: 0.6823 (tm-30) REVERT: M 120 MET cc_start: 0.7349 (mmp) cc_final: 0.6911 (mmp) REVERT: N 166 GLN cc_start: 0.5968 (tp-100) cc_final: 0.5653 (tp40) outliers start: 111 outliers final: 63 residues processed: 358 average time/residue: 0.3984 time to fit residues: 225.4583 Evaluate side-chains 296 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 231 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 B residue 46 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 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE 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 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 174 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 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 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 249 GLU 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: 0.9990 chunk 225 optimal weight: 0.1980 chunk 307 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 236 optimal weight: 0.2980 chunk 223 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 257 optimal weight: 40.0000 chunk 262 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.165599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.129166 restraints weight = 54781.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124716 restraints weight = 86287.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122477 restraints weight = 61938.314| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 29472 Z= 0.111 Angle : 0.534 11.735 40016 Z= 0.277 Chirality : 0.039 0.250 4484 Planarity : 0.003 0.039 5032 Dihedral : 4.839 38.668 4372 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.42 % Allowed : 16.90 % Favored : 80.68 % 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: 0.47 (0.14), residues: 3520 helix: 2.82 (0.23), residues: 460 sheet: 0.98 (0.15), residues: 1204 loop : -0.84 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 24 HIS 0.008 0.001 HIS F 105 PHE 0.024 0.001 PHE J 128 TYR 0.021 0.001 TYR G 71 ARG 0.007 0.000 ARG D 96 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 16) link_NAG-ASN : angle 2.31866 ( 48) link_BETA1-4 : bond 0.00844 ( 8) link_BETA1-4 : angle 1.46276 ( 24) hydrogen bonds : bond 0.04617 ( 918) hydrogen bonds : angle 4.72724 ( 2652) SS BOND : bond 0.00323 ( 64) SS BOND : angle 1.47553 ( 128) covalent geometry : bond 0.00248 (29384) covalent geometry : angle 0.52186 (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 336 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 258 time to evaluate : 3.429 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: 0.7284 (tmm) cc_final: 0.6820 (tpp) REVERT: A 119 MET cc_start: 0.8297 (tpt) cc_final: 0.8097 (tpt) REVERT: A 157 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: A 168 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8054 (mm-40) REVERT: A 210 ASP cc_start: 0.8558 (t0) cc_final: 0.8298 (t0) REVERT: D 58 ASP cc_start: 0.7721 (t0) cc_final: 0.7401 (t0) REVERT: E 210 ASP cc_start: 0.8155 (t0) cc_final: 0.7857 (t0) REVERT: F 26 LEU cc_start: 0.5890 (tt) cc_final: 0.5443 (tp) REVERT: F 117 LEU cc_start: 0.5525 (OUTLIER) cc_final: 0.5139 (mt) REVERT: F 194 GLN cc_start: 0.6730 (tm-30) cc_final: 0.5934 (tm-30) REVERT: G 253 LEU cc_start: 0.8208 (mm) cc_final: 0.7520 (tp) REVERT: J 194 GLN cc_start: 0.7474 (tm-30) cc_final: 0.6687 (tm-30) REVERT: M 120 MET cc_start: 0.7259 (mmp) cc_final: 0.6860 (mmp) REVERT: M 175 GLU cc_start: 0.7311 (tp30) cc_final: 0.7004 (tp30) REVERT: N 117 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7633 (mm) REVERT: N 166 GLN cc_start: 0.5943 (tp-100) cc_final: 0.5722 (tp40) outliers start: 78 outliers final: 50 residues processed: 315 average time/residue: 0.4200 time to fit residues: 209.0072 Evaluate side-chains 288 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 235 time to evaluate : 3.075 ------------------------------------------------------------------------------- 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 191 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 32 ASP 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 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 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 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain J residue 117 LEU 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: 2.9990 chunk 208 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 130 optimal weight: 0.0070 chunk 315 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 339 optimal weight: 4.9990 chunk 309 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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** K 81 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.163286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.115835 restraints weight = 55483.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111536 restraints weight = 48773.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112610 restraints weight = 45698.366| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 29472 Z= 0.114 Angle : 0.526 13.727 40016 Z= 0.272 Chirality : 0.039 0.271 4484 Planarity : 0.003 0.044 5032 Dihedral : 4.620 36.782 4372 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.61 % Allowed : 16.72 % Favored : 80.68 % 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: 2.95 (0.23), residues: 460 sheet: 0.93 (0.15), residues: 1220 loop : -0.79 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 228 HIS 0.007 0.001 HIS F 105 PHE 0.027 0.001 PHE J 128 TYR 0.023 0.001 TYR F 220 ARG 0.010 0.000 ARG G 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 16) link_NAG-ASN : angle 2.24861 ( 48) link_BETA1-4 : bond 0.00779 ( 8) link_BETA1-4 : angle 1.45295 ( 24) hydrogen bonds : bond 0.04408 ( 918) hydrogen bonds : angle 4.57604 ( 2652) SS BOND : bond 0.00310 ( 64) SS BOND : angle 1.42039 ( 128) covalent geometry : bond 0.00262 (29384) covalent geometry : angle 0.51388 (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 329 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 245 time to evaluate : 3.230 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: 0.7318 (tmm) cc_final: 0.6897 (tpp) REVERT: A 88 LEU cc_start: 0.8435 (pt) cc_final: 0.7989 (mm) REVERT: A 157 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7355 (mp10) REVERT: D 58 ASP cc_start: 0.8005 (t0) cc_final: 0.7627 (t0) REVERT: D 98 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7296 (mm-40) REVERT: E 210 ASP cc_start: 0.8341 (t0) cc_final: 0.7966 (t0) REVERT: F 26 LEU cc_start: 0.6573 (tt) cc_final: 0.6218 (tp) REVERT: F 117 LEU cc_start: 0.5162 (OUTLIER) cc_final: 0.4819 (mt) REVERT: G 253 LEU cc_start: 0.8276 (mm) cc_final: 0.7519 (tp) REVERT: J 194 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6538 (tm-30) REVERT: M 120 MET cc_start: 0.7118 (mmp) cc_final: 0.6685 (mmp) REVERT: M 175 GLU cc_start: 0.7373 (tp30) cc_final: 0.7140 (tp30) REVERT: N 117 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7424 (mm) REVERT: N 166 GLN cc_start: 0.6063 (tp-100) cc_final: 0.5734 (tp40) REVERT: O 100 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.9097 (m) outliers start: 84 outliers final: 63 residues processed: 314 average time/residue: 0.4059 time to fit residues: 202.2494 Evaluate side-chains 296 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 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 86 ASN 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 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 299 ILE 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 298 LEU Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain 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 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 270 SER 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 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: 0.7980 chunk 233 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 198 optimal weight: 0.0040 chunk 17 optimal weight: 0.9980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.162892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115642 restraints weight = 55392.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111368 restraints weight = 49207.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111851 restraints weight = 46291.639| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4599 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= 0.118 Angle : 0.518 11.745 40016 Z= 0.269 Chirality : 0.039 0.256 4484 Planarity : 0.003 0.041 5032 Dihedral : 4.519 36.950 4372 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.70 % Allowed : 16.66 % Favored : 80.65 % 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: 0.49 (0.14), residues: 3520 helix: 2.97 (0.23), residues: 460 sheet: 0.90 (0.15), residues: 1220 loop : -0.79 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 60 HIS 0.011 0.001 HIS F 105 PHE 0.023 0.001 PHE N 128 TYR 0.019 0.001 TYR J 220 ARG 0.009 0.000 ARG E 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 16) link_NAG-ASN : angle 2.21405 ( 48) link_BETA1-4 : bond 0.00765 ( 8) link_BETA1-4 : angle 1.42716 ( 24) hydrogen bonds : bond 0.04342 ( 918) hydrogen bonds : angle 4.51499 ( 2652) SS BOND : bond 0.00248 ( 64) SS BOND : angle 1.32962 ( 128) covalent geometry : bond 0.00272 (29384) covalent geometry : angle 0.50689 (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 320 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 233 time to evaluate : 3.090 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: 0.7307 (tmm) cc_final: 0.6919 (tpp) REVERT: A 88 LEU cc_start: 0.8436 (pt) cc_final: 0.7984 (mm) REVERT: A 157 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: B 157 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8122 (mtmm) REVERT: E 120 MET cc_start: 0.7116 (mmp) cc_final: 0.6619 (mmp) REVERT: E 210 ASP cc_start: 0.8328 (t0) cc_final: 0.7923 (t0) REVERT: F 26 LEU cc_start: 0.6521 (tt) cc_final: 0.6249 (tp) REVERT: F 117 LEU cc_start: 0.5084 (OUTLIER) cc_final: 0.4753 (mt) REVERT: G 253 LEU cc_start: 0.8282 (mm) cc_final: 0.7533 (tp) REVERT: G 259 TYR cc_start: 0.6870 (p90) cc_final: 0.6490 (p90) REVERT: G 269 MET cc_start: 0.5816 (pmm) cc_final: 0.5437 (pmm) REVERT: J 24 TRP cc_start: 0.6763 (p-90) cc_final: 0.6450 (p-90) REVERT: J 194 GLN cc_start: 0.7271 (tm-30) cc_final: 0.6565 (tm-30) REVERT: M 120 MET cc_start: 0.7137 (mmp) cc_final: 0.6723 (mmp) REVERT: M 175 GLU cc_start: 0.7396 (tp30) cc_final: 0.7183 (tp30) REVERT: N 117 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7460 (mm) REVERT: N 166 GLN cc_start: 0.6055 (tp-100) cc_final: 0.5714 (tp40) REVERT: O 100 VAL cc_start: 0.9346 (OUTLIER) cc_final: 0.9108 (m) outliers start: 87 outliers final: 67 residues processed: 301 average time/residue: 0.3964 time to fit residues: 189.9902 Evaluate side-chains 300 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 228 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE 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 111 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER 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 86 ASN 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 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 306 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 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 100 SER Chi-restraints excluded: chain N residue 117 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 133 optimal weight: 0.2980 chunk 327 optimal weight: 1.9990 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: 0.9990 chunk 159 optimal weight: 10.0000 chunk 182 optimal weight: 0.5980 chunk 321 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.163446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116581 restraints weight = 55642.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112978 restraints weight = 51983.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113777 restraints weight = 44707.922| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 29472 Z= 0.103 Angle : 0.501 14.777 40016 Z= 0.259 Chirality : 0.038 0.239 4484 Planarity : 0.003 0.042 5032 Dihedral : 4.280 37.439 4368 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.26 % Allowed : 17.15 % Favored : 80.58 % 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: 0.59 (0.14), residues: 3520 helix: 3.11 (0.23), residues: 472 sheet: 0.93 (0.15), residues: 1228 loop : -0.76 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 60 HIS 0.007 0.001 HIS B 91 PHE 0.020 0.001 PHE J 128 TYR 0.023 0.001 TYR F 220 ARG 0.008 0.000 ARG F 179 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 16) link_NAG-ASN : angle 2.04124 ( 48) link_BETA1-4 : bond 0.00759 ( 8) link_BETA1-4 : angle 1.41536 ( 24) hydrogen bonds : bond 0.04063 ( 918) hydrogen bonds : angle 4.34907 ( 2652) SS BOND : bond 0.00292 ( 64) SS BOND : angle 1.20112 ( 128) covalent geometry : bond 0.00233 (29384) covalent geometry : angle 0.49105 (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 314 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 241 time to evaluate : 3.032 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: A 34 MET cc_start: 0.7316 (tmm) cc_final: 0.7040 (tpp) REVERT: A 88 LEU cc_start: 0.8427 (pt) cc_final: 0.7973 (mm) REVERT: A 157 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: B 157 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7909 (mtmm) REVERT: B 248 ASN cc_start: 0.7804 (m110) cc_final: 0.7508 (m110) REVERT: D 58 ASP cc_start: 0.7728 (t0) cc_final: 0.7446 (t0) REVERT: E 120 MET cc_start: 0.7163 (mmp) cc_final: 0.6702 (mmp) REVERT: E 210 ASP cc_start: 0.8325 (t0) cc_final: 0.7970 (t0) REVERT: F 26 LEU cc_start: 0.6519 (tt) cc_final: 0.6091 (tp) REVERT: F 117 LEU cc_start: 0.5230 (OUTLIER) cc_final: 0.4859 (mt) REVERT: G 259 TYR cc_start: 0.6763 (p90) cc_final: 0.6472 (p90) REVERT: G 269 MET cc_start: 0.5978 (pmm) cc_final: 0.5768 (pmm) REVERT: J 194 GLN cc_start: 0.7350 (tm-30) cc_final: 0.6752 (tm-30) REVERT: M 120 MET cc_start: 0.7170 (mmp) cc_final: 0.6753 (mmp) REVERT: M 133 MET cc_start: 0.7691 (mtp) cc_final: 0.7442 (mtp) REVERT: N 117 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7496 (mm) REVERT: N 166 GLN cc_start: 0.5949 (tp-100) cc_final: 0.5660 (tp40) REVERT: O 100 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9096 (m) outliers start: 73 outliers final: 55 residues processed: 299 average time/residue: 0.3909 time to fit residues: 186.2575 Evaluate side-chains 292 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 232 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE 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 111 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 140 THR 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 117 LEU Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 140 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 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 L residue 123 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 102 optimal weight: 0.3980 chunk 279 optimal weight: 0.0980 chunk 163 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 345 optimal weight: 5.9990 chunk 11 optimal weight: 0.0060 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 F 166 GLN I 179 GLN ** K 134 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 = 0.4229 r_free = 0.4229 target = 0.163022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114415 restraints weight = 56097.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114560 restraints weight = 43606.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114421 restraints weight = 36698.924| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 29472 Z= 0.106 Angle : 0.508 14.411 40016 Z= 0.261 Chirality : 0.038 0.258 4484 Planarity : 0.003 0.038 5032 Dihedral : 4.225 37.590 4364 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.42 % Allowed : 17.25 % 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: 0.60 (0.14), residues: 3520 helix: 3.13 (0.23), residues: 472 sheet: 0.95 (0.15), residues: 1220 loop : -0.76 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 24 HIS 0.010 0.001 HIS F 105 PHE 0.016 0.001 PHE N 128 TYR 0.033 0.001 TYR J 220 ARG 0.008 0.000 ARG F 179 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 16) link_NAG-ASN : angle 1.95794 ( 48) link_BETA1-4 : bond 0.00745 ( 8) link_BETA1-4 : angle 1.41564 ( 24) hydrogen bonds : bond 0.04055 ( 918) hydrogen bonds : angle 4.32050 ( 2652) SS BOND : bond 0.00287 ( 64) SS BOND : angle 1.24372 ( 128) covalent geometry : bond 0.00244 (29384) covalent geometry : angle 0.49865 (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 311 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 233 time to evaluate : 4.481 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: A 34 MET cc_start: 0.7293 (tmm) cc_final: 0.7027 (tpp) REVERT: A 88 LEU cc_start: 0.8441 (pt) cc_final: 0.7992 (mm) REVERT: A 157 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: A 167 MET cc_start: 0.8414 (mtp) cc_final: 0.8177 (ttm) REVERT: B 31 TYR cc_start: 0.7208 (m-80) cc_final: 0.6900 (m-80) REVERT: B 157 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7930 (mtmm) REVERT: D 58 ASP cc_start: 0.7722 (t0) cc_final: 0.7476 (t0) REVERT: E 120 MET cc_start: 0.7126 (mmp) cc_final: 0.6679 (mmp) REVERT: E 210 ASP cc_start: 0.8336 (t0) cc_final: 0.7898 (t0) REVERT: F 26 LEU cc_start: 0.6523 (tt) cc_final: 0.6211 (tp) REVERT: F 117 LEU cc_start: 0.5131 (OUTLIER) cc_final: 0.4785 (mt) REVERT: G 259 TYR cc_start: 0.6856 (p90) cc_final: 0.6471 (p90) REVERT: G 269 MET cc_start: 0.5906 (pmm) cc_final: 0.5653 (pmm) REVERT: J 194 GLN cc_start: 0.7265 (tm-30) cc_final: 0.6717 (tm-30) REVERT: M 120 MET cc_start: 0.7136 (mmp) cc_final: 0.6743 (mmp) REVERT: N 117 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7437 (mm) REVERT: O 100 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.9078 (m) outliers start: 78 outliers final: 63 residues processed: 295 average time/residue: 0.3998 time to fit residues: 190.3109 Evaluate side-chains 290 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE 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 99 HIS Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER 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 140 THR Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain D residue 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 307 SER Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 301 TYR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 82 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 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 270 SER 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 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 O residue 298 LEU 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: 0.0870 chunk 291 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 320 optimal weight: 4.9990 chunk 208 optimal weight: 0.2980 chunk 347 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.4764 ------------------------------------------------------------------------------- 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 I 179 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.161108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111937 restraints weight = 55439.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110359 restraints weight = 40659.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109796 restraints weight = 38305.649| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29472 Z= 0.160 Angle : 0.547 14.285 40016 Z= 0.284 Chirality : 0.039 0.245 4484 Planarity : 0.004 0.038 5032 Dihedral : 4.440 36.917 4364 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.20 % Allowed : 17.37 % Favored : 80.43 % 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: 2.93 (0.23), residues: 472 sheet: 0.92 (0.15), residues: 1196 loop : -0.78 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 60 HIS 0.009 0.001 HIS F 105 PHE 0.019 0.002 PHE O 73 TYR 0.026 0.001 TYR J 220 ARG 0.010 0.000 ARG O 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 16) link_NAG-ASN : angle 2.27160 ( 48) link_BETA1-4 : bond 0.00603 ( 8) link_BETA1-4 : angle 1.33776 ( 24) hydrogen bonds : bond 0.04724 ( 918) hydrogen bonds : angle 4.51014 ( 2652) SS BOND : bond 0.00329 ( 64) SS BOND : angle 1.19949 ( 128) covalent geometry : bond 0.00377 (29384) covalent geometry : angle 0.53742 (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 309 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 238 time to evaluate : 3.063 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: 0.7139 (tmm) cc_final: 0.6924 (tpp) REVERT: A 88 LEU cc_start: 0.8472 (pt) cc_final: 0.8009 (mm) REVERT: A 157 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: B 31 TYR cc_start: 0.7303 (m-80) cc_final: 0.6986 (m-80) REVERT: B 45 MET cc_start: 0.6291 (mmm) cc_final: 0.6040 (mmm) REVERT: E 210 ASP cc_start: 0.8421 (t0) cc_final: 0.7983 (t0) REVERT: F 26 LEU cc_start: 0.6648 (tt) cc_final: 0.6428 (tp) REVERT: F 103 LEU cc_start: 0.6063 (mm) cc_final: 0.5820 (mm) REVERT: F 117 LEU cc_start: 0.5002 (OUTLIER) cc_final: 0.4657 (mt) REVERT: G 259 TYR cc_start: 0.7028 (p90) cc_final: 0.6627 (p90) REVERT: G 269 MET cc_start: 0.6155 (pmm) cc_final: 0.5932 (pmm) REVERT: J 24 TRP cc_start: 0.6972 (p-90) cc_final: 0.6497 (p-90) REVERT: J 194 GLN cc_start: 0.7225 (tm-30) cc_final: 0.6663 (tm-30) REVERT: K 253 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8457 (tt) REVERT: M 120 MET cc_start: 0.7191 (mmp) cc_final: 0.6797 (mmp) REVERT: N 117 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7201 (mm) REVERT: O 100 VAL cc_start: 0.9338 (OUTLIER) cc_final: 0.9110 (m) outliers start: 71 outliers final: 60 residues processed: 295 average time/residue: 0.3743 time to fit residues: 178.6281 Evaluate side-chains 286 residues out of total 3224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 221 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE 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 109 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 276 LYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 117 LEU 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 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 253 LEU 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 270 SER 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 129 ASN Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 290 TYR Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain O residue 298 LEU 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: 0.9980 chunk 303 optimal weight: 0.0570 chunk 329 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 305 optimal weight: 1.9990 chunk 347 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 271 optimal weight: 0.8980 overall best weight: 0.7700 ------------------------------------------------------------------------------- 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 57 GLN E 157 GLN G 66 ASN I 179 GLN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 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 = 0.4215 r_free = 0.4215 target = 0.162377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.113820 restraints weight = 55188.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110478 restraints weight = 46672.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111217 restraints weight = 42564.605| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29472 Z= 0.113 Angle : 0.513 14.313 40016 Z= 0.265 Chirality : 0.038 0.238 4484 Planarity : 0.003 0.038 5032 Dihedral : 4.242 36.854 4360 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.08 % Allowed : 17.71 % Favored : 80.21 % 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: 2.97 (0.24), residues: 460 sheet: 0.94 (0.15), residues: 1196 loop : -0.77 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP F 24 HIS 0.010 0.001 HIS F 105 PHE 0.014 0.001 PHE N 128 TYR 0.028 0.001 TYR J 220 ARG 0.010 0.000 ARG E 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 16) link_NAG-ASN : angle 1.98995 ( 48) link_BETA1-4 : bond 0.00712 ( 8) link_BETA1-4 : angle 1.36521 ( 24) hydrogen bonds : bond 0.04257 ( 918) hydrogen bonds : angle 4.35776 ( 2652) SS BOND : bond 0.00311 ( 64) SS BOND : angle 1.12701 ( 128) covalent geometry : bond 0.00260 (29384) covalent geometry : angle 0.50482 (39816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9510.38 seconds wall clock time: 167 minutes 48.68 seconds (10068.68 seconds total)