Starting phenix.real_space_refine on Wed Jan 14 22:44:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ugq_42232/01_2026/8ugq_42232.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ugq_42232/01_2026/8ugq_42232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ugq_42232/01_2026/8ugq_42232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ugq_42232/01_2026/8ugq_42232.map" model { file = "/net/cci-nas-00/data/ceres_data/8ugq_42232/01_2026/8ugq_42232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ugq_42232/01_2026/8ugq_42232.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 88 5.16 5 C 12466 2.51 5 N 3678 2.21 5 O 3893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20222 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1664 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "L" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1673 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 203} Chain: "M" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain: "N" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 161 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "D" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1664 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "O" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1664 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "P" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 179 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1664 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "Q" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "G" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1664 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "R" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 179 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1638 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain: "S" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "I" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain: "T" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "J" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1673 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 203} Chain: "U" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "K" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain: "V" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 4.87, per 1000 atoms: 0.24 Number of scatterers: 20222 At special positions: 0 Unit cell: (157.56, 122.21, 210.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 97 15.00 O 3893 8.00 N 3678 7.00 C 12466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 902.2 milliseconds 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4216 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 33 sheets defined 10.4% alpha, 48.5% beta 0 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.792A pdb=" N THR A 140 " --> pdb=" O TRP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 131 through 135 Processing helix chain 'B' and resid 137 through 141 removed outlier: 3.791A pdb=" N THR B 140 " --> pdb=" O TRP B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.701A pdb=" N ARG C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 145 through 149 removed outlier: 4.590A pdb=" N HIS C 149 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 131 through 135 Processing helix chain 'D' and resid 137 through 141 removed outlier: 3.791A pdb=" N THR D 140 " --> pdb=" O TRP D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 137 through 141 removed outlier: 3.792A pdb=" N THR E 140 " --> pdb=" O TRP E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 131 through 135 Processing helix chain 'F' and resid 137 through 141 removed outlier: 3.791A pdb=" N THR F 140 " --> pdb=" O TRP F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'G' and resid 123 through 128 Processing helix chain 'G' and resid 131 through 135 Processing helix chain 'G' and resid 137 through 141 removed outlier: 3.792A pdb=" N THR G 140 " --> pdb=" O TRP G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'H' and resid 123 through 128 Processing helix chain 'H' and resid 131 through 135 Processing helix chain 'H' and resid 137 through 141 removed outlier: 3.792A pdb=" N THR H 140 " --> pdb=" O TRP H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 209 No H-bonds generated for 'chain 'H' and resid 207 through 209' Processing helix chain 'I' and resid 48 through 52 Processing helix chain 'I' and resid 123 through 128 Processing helix chain 'I' and resid 131 through 135 Processing helix chain 'I' and resid 137 through 141 removed outlier: 3.791A pdb=" N THR I 140 " --> pdb=" O TRP I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 209 No H-bonds generated for 'chain 'I' and resid 207 through 209' Processing helix chain 'J' and resid 97 through 101 removed outlier: 3.522A pdb=" N ARG J 100 " --> pdb=" O ALA J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 131 through 135 Processing helix chain 'J' and resid 137 through 141 removed outlier: 3.792A pdb=" N THR J 140 " --> pdb=" O TRP J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 209 No H-bonds generated for 'chain 'J' and resid 207 through 209' Processing helix chain 'K' and resid 123 through 128 Processing helix chain 'K' and resid 131 through 135 Processing helix chain 'K' and resid 137 through 141 removed outlier: 3.792A pdb=" N THR K 140 " --> pdb=" O TRP K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 209 No H-bonds generated for 'chain 'K' and resid 207 through 209' Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 47 removed outlier: 3.522A pdb=" N GLN A 43 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A 229 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE A 92 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS A 231 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR A 90 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN A 233 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE A 88 " --> pdb=" O GLN A 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG A 235 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE A 86 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR A 237 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 82 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 80 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 removed outlier: 4.016A pdb=" N PHE A 228 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A 229 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE A 92 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS A 231 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR A 90 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN A 233 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE A 88 " --> pdb=" O GLN A 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG A 235 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE A 86 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR A 237 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 82 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 80 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 81 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 196 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN A 199 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 63 removed outlier: 7.114A pdb=" N ASN A 103 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU A 162 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY A 105 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN A 160 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY A 107 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU A 158 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET A 109 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG A 156 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 111 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 47 removed outlier: 3.620A pdb=" N PHE B 238 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 43 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR B 229 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE B 92 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS B 231 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR B 90 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN B 233 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE B 88 " --> pdb=" O GLN B 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG B 235 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE B 86 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR B 237 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 82 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 80 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 54 through 55 removed outlier: 4.016A pdb=" N PHE B 228 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR B 229 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE B 92 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS B 231 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR B 90 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN B 233 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE B 88 " --> pdb=" O GLN B 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG B 235 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE B 86 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR B 237 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 82 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 80 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 81 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 196 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN B 199 " --> pdb=" O GLN B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 63 removed outlier: 7.115A pdb=" N ASN B 103 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU B 162 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY B 105 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN B 160 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY B 107 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU B 158 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET B 109 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG B 156 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 111 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 47 removed outlier: 7.355A pdb=" N GLN C 233 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE C 88 " --> pdb=" O GLN C 233 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG C 235 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE C 86 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 237 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU C 80 " --> pdb=" O VAL C 241 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.928A pdb=" N PHE C 228 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN C 199 " --> pdb=" O GLN C 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 63 removed outlier: 3.555A pdb=" N ASP C 62 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 108 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG C 155 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR C 113 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL C 153 " --> pdb=" O TYR C 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 41 through 47 removed outlier: 3.521A pdb=" N GLN D 43 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR D 229 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE D 92 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS D 231 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR D 90 " --> pdb=" O HIS D 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN D 233 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE D 88 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG D 235 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE D 86 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR D 237 " --> pdb=" O TYR D 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 54 through 55 removed outlier: 4.016A pdb=" N PHE D 228 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR D 229 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE D 92 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS D 231 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR D 90 " --> pdb=" O HIS D 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN D 233 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE D 88 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG D 235 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE D 86 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR D 237 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 81 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 196 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN D 199 " --> pdb=" O GLN D 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 60 through 63 removed outlier: 7.114A pdb=" N ASN D 103 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU D 162 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY D 105 " --> pdb=" O ASN D 160 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN D 160 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY D 107 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU D 158 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET D 109 " --> pdb=" O ARG D 156 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG D 156 " --> pdb=" O MET D 109 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU D 111 " --> pdb=" O LYS D 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 41 through 47 removed outlier: 3.522A pdb=" N GLN E 43 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR E 229 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE E 92 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS E 231 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR E 90 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN E 233 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE E 88 " --> pdb=" O GLN E 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG E 235 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE E 86 " --> pdb=" O ARG E 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR E 237 " --> pdb=" O TYR E 84 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU E 80 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 54 through 55 removed outlier: 4.016A pdb=" N PHE E 228 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR E 229 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE E 92 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS E 231 " --> pdb=" O TYR E 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR E 90 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN E 233 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE E 88 " --> pdb=" O GLN E 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG E 235 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE E 86 " --> pdb=" O ARG E 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR E 237 " --> pdb=" O TYR E 84 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU E 80 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 81 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 196 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN E 199 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 60 through 63 removed outlier: 7.115A pdb=" N ASN E 103 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU E 162 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY E 105 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN E 160 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY E 107 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU E 158 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET E 109 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG E 156 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU E 111 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 41 through 47 removed outlier: 3.521A pdb=" N GLN F 43 " --> pdb=" O LEU F 236 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR F 229 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE F 92 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS F 231 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR F 90 " --> pdb=" O HIS F 231 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN F 233 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE F 88 " --> pdb=" O GLN F 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG F 235 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE F 86 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR F 237 " --> pdb=" O TYR F 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 54 through 55 removed outlier: 4.017A pdb=" N PHE F 228 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR F 229 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE F 92 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS F 231 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR F 90 " --> pdb=" O HIS F 231 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN F 233 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE F 88 " --> pdb=" O GLN F 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG F 235 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE F 86 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR F 237 " --> pdb=" O TYR F 84 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR F 81 " --> pdb=" O THR F 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL F 196 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN F 199 " --> pdb=" O GLN F 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 60 through 63 removed outlier: 7.114A pdb=" N ASN F 103 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU F 162 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY F 105 " --> pdb=" O ASN F 160 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN F 160 " --> pdb=" O GLY F 105 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY F 107 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU F 158 " --> pdb=" O GLY F 107 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET F 109 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG F 156 " --> pdb=" O MET F 109 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU F 111 " --> pdb=" O LYS F 154 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 41 through 47 removed outlier: 3.521A pdb=" N GLN G 43 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 229 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE G 92 " --> pdb=" O THR G 229 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N HIS G 231 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR G 90 " --> pdb=" O HIS G 231 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN G 233 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE G 88 " --> pdb=" O GLN G 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG G 235 " --> pdb=" O ILE G 86 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE G 86 " --> pdb=" O ARG G 235 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR G 237 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU G 82 " --> pdb=" O LYS G 239 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU G 80 " --> pdb=" O VAL G 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 54 through 55 removed outlier: 4.017A pdb=" N PHE G 228 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 229 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE G 92 " --> pdb=" O THR G 229 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N HIS G 231 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR G 90 " --> pdb=" O HIS G 231 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN G 233 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE G 88 " --> pdb=" O GLN G 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG G 235 " --> pdb=" O ILE G 86 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE G 86 " --> pdb=" O ARG G 235 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR G 237 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU G 82 " --> pdb=" O LYS G 239 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU G 80 " --> pdb=" O VAL G 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR G 81 " --> pdb=" O THR G 198 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL G 196 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN G 199 " --> pdb=" O GLN G 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 60 through 63 removed outlier: 7.115A pdb=" N ASN G 103 " --> pdb=" O GLU G 162 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU G 162 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY G 105 " --> pdb=" O ASN G 160 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN G 160 " --> pdb=" O GLY G 105 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY G 107 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU G 158 " --> pdb=" O GLY G 107 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET G 109 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG G 156 " --> pdb=" O MET G 109 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU G 111 " --> pdb=" O LYS G 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 41 through 47 removed outlier: 3.523A pdb=" N GLN H 43 " --> pdb=" O LEU H 236 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR H 229 " --> pdb=" O PHE H 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE H 92 " --> pdb=" O THR H 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS H 231 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR H 90 " --> pdb=" O HIS H 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN H 233 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE H 88 " --> pdb=" O GLN H 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG H 235 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE H 86 " --> pdb=" O ARG H 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR H 237 " --> pdb=" O TYR H 84 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU H 80 " --> pdb=" O VAL H 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 54 through 55 removed outlier: 4.016A pdb=" N PHE H 228 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR H 229 " --> pdb=" O PHE H 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE H 92 " --> pdb=" O THR H 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS H 231 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR H 90 " --> pdb=" O HIS H 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN H 233 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE H 88 " --> pdb=" O GLN H 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG H 235 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE H 86 " --> pdb=" O ARG H 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR H 237 " --> pdb=" O TYR H 84 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU H 80 " --> pdb=" O VAL H 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR H 81 " --> pdb=" O THR H 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL H 196 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN H 199 " --> pdb=" O GLN H 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 60 through 63 removed outlier: 7.115A pdb=" N ASN H 103 " --> pdb=" O GLU H 162 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU H 162 " --> pdb=" O ASN H 103 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY H 105 " --> pdb=" O ASN H 160 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN H 160 " --> pdb=" O GLY H 105 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY H 107 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU H 158 " --> pdb=" O GLY H 107 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET H 109 " --> pdb=" O ARG H 156 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG H 156 " --> pdb=" O MET H 109 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU H 111 " --> pdb=" O LYS H 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 41 through 47 removed outlier: 3.506A pdb=" N THR I 234 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY I 232 " --> pdb=" O HIS I 47 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR I 229 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE I 92 " --> pdb=" O THR I 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS I 231 " --> pdb=" O TYR I 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR I 90 " --> pdb=" O HIS I 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN I 233 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE I 88 " --> pdb=" O GLN I 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG I 235 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE I 86 " --> pdb=" O ARG I 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR I 237 " --> pdb=" O TYR I 84 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 82 " --> pdb=" O LYS I 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 41 through 47 removed outlier: 3.506A pdb=" N THR I 234 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY I 232 " --> pdb=" O HIS I 47 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR I 229 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE I 92 " --> pdb=" O THR I 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS I 231 " --> pdb=" O TYR I 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR I 90 " --> pdb=" O HIS I 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN I 233 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE I 88 " --> pdb=" O GLN I 233 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG I 235 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE I 86 " --> pdb=" O ARG I 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR I 237 " --> pdb=" O TYR I 84 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 82 " --> pdb=" O LYS I 239 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL I 196 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN I 199 " --> pdb=" O GLN I 212 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 151 through 163 removed outlier: 6.922A pdb=" N LEU I 111 " --> pdb=" O LYS I 154 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG I 156 " --> pdb=" O MET I 109 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET I 109 " --> pdb=" O ARG I 156 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU I 158 " --> pdb=" O GLY I 107 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY I 107 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN I 160 " --> pdb=" O GLY I 105 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY I 105 " --> pdb=" O ASN I 160 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU I 162 " --> pdb=" O ASN I 103 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASN I 103 " --> pdb=" O GLU I 162 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 41 through 47 removed outlier: 3.521A pdb=" N GLN J 43 " --> pdb=" O LEU J 236 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR J 229 " --> pdb=" O PHE J 92 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE J 92 " --> pdb=" O THR J 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS J 231 " --> pdb=" O TYR J 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR J 90 " --> pdb=" O HIS J 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN J 233 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE J 88 " --> pdb=" O GLN J 233 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG J 235 " --> pdb=" O ILE J 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE J 86 " --> pdb=" O ARG J 235 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR J 237 " --> pdb=" O TYR J 84 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 82 " --> pdb=" O LYS J 239 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU J 80 " --> pdb=" O VAL J 241 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 54 through 55 removed outlier: 4.016A pdb=" N PHE J 228 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR J 229 " --> pdb=" O PHE J 92 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE J 92 " --> pdb=" O THR J 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS J 231 " --> pdb=" O TYR J 90 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR J 90 " --> pdb=" O HIS J 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN J 233 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE J 88 " --> pdb=" O GLN J 233 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG J 235 " --> pdb=" O ILE J 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE J 86 " --> pdb=" O ARG J 235 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR J 237 " --> pdb=" O TYR J 84 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 82 " --> pdb=" O LYS J 239 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU J 80 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR J 81 " --> pdb=" O THR J 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL J 196 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN J 199 " --> pdb=" O GLN J 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 60 through 63 removed outlier: 7.115A pdb=" N ASN J 103 " --> pdb=" O GLU J 162 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU J 162 " --> pdb=" O ASN J 103 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY J 105 " --> pdb=" O ASN J 160 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN J 160 " --> pdb=" O GLY J 105 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY J 107 " --> pdb=" O LEU J 158 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU J 158 " --> pdb=" O GLY J 107 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET J 109 " --> pdb=" O ARG J 156 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG J 156 " --> pdb=" O MET J 109 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU J 111 " --> pdb=" O LYS J 154 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 41 through 47 removed outlier: 3.522A pdb=" N GLN K 43 " --> pdb=" O LEU K 236 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR K 229 " --> pdb=" O PHE K 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE K 92 " --> pdb=" O THR K 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS K 231 " --> pdb=" O TYR K 90 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR K 90 " --> pdb=" O HIS K 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN K 233 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE K 88 " --> pdb=" O GLN K 233 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG K 235 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE K 86 " --> pdb=" O ARG K 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR K 237 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU K 80 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 54 through 55 removed outlier: 4.016A pdb=" N PHE K 228 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR K 229 " --> pdb=" O PHE K 92 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE K 92 " --> pdb=" O THR K 229 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS K 231 " --> pdb=" O TYR K 90 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR K 90 " --> pdb=" O HIS K 231 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN K 233 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE K 88 " --> pdb=" O GLN K 233 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG K 235 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE K 86 " --> pdb=" O ARG K 235 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR K 237 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU K 80 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR K 81 " --> pdb=" O THR K 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL K 196 " --> pdb=" O THR K 83 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN K 199 " --> pdb=" O GLN K 212 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 60 through 63 removed outlier: 7.115A pdb=" N ASN K 103 " --> pdb=" O GLU K 162 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU K 162 " --> pdb=" O ASN K 103 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY K 105 " --> pdb=" O ASN K 160 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN K 160 " --> pdb=" O GLY K 105 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY K 107 " --> pdb=" O LEU K 158 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU K 158 " --> pdb=" O GLY K 107 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET K 109 " --> pdb=" O ARG K 156 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG K 156 " --> pdb=" O MET K 109 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU K 111 " --> pdb=" O LYS K 154 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6284 1.34 - 1.45: 4795 1.45 - 1.57: 9541 1.57 - 1.69: 190 1.69 - 1.81: 132 Bond restraints: 20942 Sorted by residual: bond pdb=" C3' DC Q 900 " pdb=" O3' DC Q 900 " ideal model delta sigma weight residual 1.422 1.667 -0.245 3.00e-02 1.11e+03 6.69e+01 bond pdb=" O5' DA S 908 " pdb=" C5' DA S 908 " ideal model delta sigma weight residual 1.423 1.581 -0.158 3.00e-02 1.11e+03 2.77e+01 bond pdb=" C3' DC S 900 " pdb=" O3' DC S 900 " ideal model delta sigma weight residual 1.422 1.561 -0.139 3.00e-02 1.11e+03 2.14e+01 bond pdb=" C1' DC Q 900 " pdb=" N1 DC Q 900 " ideal model delta sigma weight residual 1.490 1.621 -0.131 3.00e-02 1.11e+03 1.90e+01 bond pdb=" C3' DC U 900 " pdb=" O3' DC U 900 " ideal model delta sigma weight residual 1.422 1.304 0.118 3.00e-02 1.11e+03 1.55e+01 ... (remaining 20937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 28653 3.65 - 7.30: 166 7.30 - 10.95: 20 10.95 - 14.60: 2 14.60 - 18.25: 2 Bond angle restraints: 28843 Sorted by residual: angle pdb=" N SER A 33 " pdb=" CA SER A 33 " pdb=" C SER A 33 " ideal model delta sigma weight residual 111.28 123.19 -11.91 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N ASP A 36 " pdb=" CA ASP A 36 " pdb=" C ASP A 36 " ideal model delta sigma weight residual 111.28 122.08 -10.80 1.09e+00 8.42e-01 9.81e+01 angle pdb=" O3' DC S 900 " pdb=" C3' DC S 900 " pdb=" C2' DC S 900 " ideal model delta sigma weight residual 111.50 121.26 -9.76 1.50e+00 4.44e-01 4.23e+01 angle pdb=" C3' DC Q 900 " pdb=" O3' DC Q 900 " pdb=" P DG Q 901 " ideal model delta sigma weight residual 120.20 129.74 -9.54 1.50e+00 4.44e-01 4.05e+01 angle pdb=" C THR C 78 " pdb=" CA THR C 78 " pdb=" CB THR C 78 " ideal model delta sigma weight residual 115.79 108.24 7.55 1.19e+00 7.06e-01 4.03e+01 ... (remaining 28838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.56: 11401 27.56 - 55.12: 403 55.12 - 82.67: 148 82.67 - 110.23: 6 110.23 - 137.79: 6 Dihedral angle restraints: 11964 sinusoidal: 5311 harmonic: 6653 Sorted by residual: dihedral pdb=" CG ARG D 30 " pdb=" CD ARG D 30 " pdb=" NE ARG D 30 " pdb=" CZ ARG D 30 " ideal model delta sinusoidal sigma weight residual 90.00 0.74 89.26 2 1.50e+01 4.44e-03 2.13e+01 dihedral pdb=" N CYS I 148 " pdb=" C CYS I 148 " pdb=" CA CYS I 148 " pdb=" CB CYS I 148 " ideal model delta harmonic sigma weight residual 122.80 133.86 -11.06 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" C CYS I 148 " pdb=" N CYS I 148 " pdb=" CA CYS I 148 " pdb=" CB CYS I 148 " ideal model delta harmonic sigma weight residual -122.60 -133.27 10.67 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 11961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2998 0.089 - 0.178: 142 0.178 - 0.267: 4 0.267 - 0.356: 3 0.356 - 0.445: 1 Chirality restraints: 3148 Sorted by residual: chirality pdb=" CA CYS I 148 " pdb=" N CYS I 148 " pdb=" C CYS I 148 " pdb=" CB CYS I 148 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.45 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CA SER A 33 " pdb=" N SER A 33 " pdb=" C SER A 33 " pdb=" CB SER A 33 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C3' DC Q 900 " pdb=" C4' DC Q 900 " pdb=" O3' DC Q 900 " pdb=" C2' DC Q 900 " both_signs ideal model delta sigma weight residual False -2.66 -2.97 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 3145 not shown) Planarity restraints: 3378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 37 " -0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO C 38 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 38 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 38 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 37 " -0.052 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO D 38 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 38 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 38 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC V 900 " 0.030 2.00e-02 2.50e+03 1.53e-02 5.24e+00 pdb=" N1 DC V 900 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DC V 900 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DC V 900 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DC V 900 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC V 900 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC V 900 " 0.017 2.00e-02 2.50e+03 pdb=" C5 DC V 900 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC V 900 " -0.005 2.00e-02 2.50e+03 ... (remaining 3375 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 686 2.68 - 3.24: 18773 3.24 - 3.79: 29204 3.79 - 4.35: 36631 4.35 - 4.90: 63103 Nonbonded interactions: 148397 Sorted by model distance: nonbonded pdb=" N4 DC V 900 " pdb=" O2 DC V 907 " model vdw 2.129 3.120 nonbonded pdb=" N9 DA P 908 " pdb=" C5 DA P 908 " model vdw 2.206 2.672 nonbonded pdb=" CB ALA A 35 " pdb=" CD2 LEU A 40 " model vdw 2.221 3.880 nonbonded pdb=" OD1 ASP K 205 " pdb=" N GLY K 206 " model vdw 2.335 3.120 nonbonded pdb=" OD1 ASP B 205 " pdb=" N GLY B 206 " model vdw 2.335 3.120 ... (remaining 148392 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 34 through 243) selection = (chain 'B' and resid 34 through 243) selection = (chain 'C' and resid 34 through 243) selection = (chain 'D' and resid 34 through 243) selection = (chain 'E' and resid 34 through 243) selection = (chain 'F' and resid 34 through 243) selection = (chain 'G' and resid 34 through 243) selection = chain 'H' selection = (chain 'I' and resid 34 through 243) selection = (chain 'J' and resid 34 through 243) selection = (chain 'K' and resid 34 through 243) } ncs_group { reference = (chain 'L' and (resid 901 through 907 or (resid 908 and (name P or name OP1 or n \ ame OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' \ or name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 o \ r name N6 or name N1 or name C2 or name N3 )))) selection = (chain 'M' and (resid 901 through 907 or (resid 908 and (name P or name OP1 or n \ ame OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' \ or name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 o \ r name N6 or name N1 or name C2 or name N3 )))) selection = (chain 'N' and (resid 901 through 907 or (resid 908 and (name P or name OP1 or n \ ame OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' \ or name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 o \ r name N6 or name N1 or name C2 or name N3 )))) selection = (chain 'O' and (resid 901 through 907 or (resid 908 and (name P or name OP1 or n \ ame OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' \ or name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 o \ r name N6 or name N1 or name C2 or name N3 )))) selection = (chain 'P' and resid 901 through 908) selection = (chain 'Q' and (resid 901 through 907 or (resid 908 and (name P or name OP1 or n \ ame OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' \ or name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 o \ r name N6 or name N1 or name C2 or name N3 )))) selection = (chain 'R' and (resid 901 through 907 or (resid 908 and (name P or name OP1 or n \ ame OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' \ or name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 o \ r name N6 or name N1 or name C2 or name N3 )))) selection = (chain 'S' and (resid 901 through 907 or (resid 908 and (name P or name OP1 or n \ ame OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' \ or name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 o \ r name N6 or name N1 or name C2 or name N3 )))) selection = (chain 'T' and (resid 901 through 907 or (resid 908 and (name P or name OP1 or n \ ame OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' \ or name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 o \ r name N6 or name N1 or name C2 or name N3 )))) selection = (chain 'U' and (resid 901 through 907 or (resid 908 and (name P or name OP1 or n \ ame OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' \ or name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 o \ r name N6 or name N1 or name C2 or name N3 )))) selection = (chain 'V' and (resid 901 through 907 or (resid 908 and (name P or name OP1 or n \ ame OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or name O3' \ or name C2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 o \ r name N6 or name N1 or name C2 or name N3 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.510 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.008 0.245 20942 Z= 0.392 Angle : 0.901 18.247 28843 Z= 0.552 Chirality : 0.046 0.445 3148 Planarity : 0.005 0.088 3378 Dihedral : 15.833 137.788 7748 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.43 % Favored : 95.36 % Rotamer: Outliers : 0.26 % Allowed : 2.15 % Favored : 97.59 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.14), residues: 2327 helix: -4.02 (0.21), residues: 180 sheet: -1.76 (0.14), residues: 947 loop : -2.04 (0.14), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 235 TYR 0.014 0.002 TYR C 67 PHE 0.011 0.002 PHE C 187 TRP 0.033 0.003 TRP D 178 HIS 0.007 0.001 HIS F 91 Details of bonding type rmsd covalent geometry : bond 0.00831 (20942) covalent geometry : angle 0.90065 (28843) hydrogen bonds : bond 0.33115 ( 476) hydrogen bonds : angle 10.05982 ( 1299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 645 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.8915 (t0) cc_final: 0.8624 (t0) REVERT: A 67 TYR cc_start: 0.8779 (m-80) cc_final: 0.8513 (m-10) REVERT: A 73 GLU cc_start: 0.8231 (pm20) cc_final: 0.7925 (pm20) REVERT: A 80 GLU cc_start: 0.7938 (tt0) cc_final: 0.7732 (tt0) REVERT: A 120 GLN cc_start: 0.7558 (pt0) cc_final: 0.7338 (tm-30) REVERT: A 175 ASN cc_start: 0.7749 (t0) cc_final: 0.7465 (t0) REVERT: A 203 VAL cc_start: 0.8713 (t) cc_final: 0.8447 (p) REVERT: A 205 ASP cc_start: 0.8588 (t0) cc_final: 0.8267 (t0) REVERT: B 113 TYR cc_start: 0.8805 (t80) cc_final: 0.8584 (t80) REVERT: B 120 GLN cc_start: 0.7818 (tp40) cc_final: 0.7558 (pm20) REVERT: B 175 ASN cc_start: 0.8467 (t0) cc_final: 0.8266 (t0) REVERT: C 65 ASN cc_start: 0.8439 (t0) cc_final: 0.8175 (t0) REVERT: C 82 LEU cc_start: 0.8965 (mt) cc_final: 0.8733 (mt) REVERT: D 41 GLN cc_start: 0.9149 (mt0) cc_final: 0.8929 (mt0) REVERT: D 78 THR cc_start: 0.8505 (p) cc_final: 0.8257 (p) REVERT: D 169 SER cc_start: 0.8971 (m) cc_final: 0.8736 (p) REVERT: D 175 ASN cc_start: 0.8757 (t0) cc_final: 0.8543 (t0) REVERT: D 205 ASP cc_start: 0.8833 (t0) cc_final: 0.8538 (t0) REVERT: D 220 ILE cc_start: 0.9296 (mm) cc_final: 0.9044 (mm) REVERT: E 34 LYS cc_start: 0.6988 (mmtt) cc_final: 0.6685 (mmtp) REVERT: E 62 ASP cc_start: 0.8639 (t0) cc_final: 0.8336 (t70) REVERT: E 67 TYR cc_start: 0.8837 (m-80) cc_final: 0.8540 (m-10) REVERT: E 75 ASN cc_start: 0.8509 (m-40) cc_final: 0.8060 (m-40) REVERT: E 80 GLU cc_start: 0.8093 (tt0) cc_final: 0.7869 (tt0) REVERT: E 99 CYS cc_start: 0.7930 (m) cc_final: 0.7659 (m) REVERT: E 201 LYS cc_start: 0.8514 (mttt) cc_final: 0.7938 (mtmm) REVERT: G 62 ASP cc_start: 0.8481 (t0) cc_final: 0.8250 (t0) REVERT: G 67 TYR cc_start: 0.8863 (m-80) cc_final: 0.8483 (m-80) REVERT: G 217 TYR cc_start: 0.9140 (m-80) cc_final: 0.8855 (m-80) REVERT: G 239 LYS cc_start: 0.9082 (ptmt) cc_final: 0.8861 (ptpt) REVERT: H 69 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7812 (tmm-80) REVERT: H 164 ASP cc_start: 0.8368 (p0) cc_final: 0.8081 (p0) REVERT: I 75 ASN cc_start: 0.8444 (m-40) cc_final: 0.8139 (m-40) REVERT: K 43 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8606 (tp-100) REVERT: K 101 TYR cc_start: 0.8030 (m-80) cc_final: 0.7314 (m-80) REVERT: K 199 GLN cc_start: 0.8432 (mt0) cc_final: 0.8201 (mp10) REVERT: K 205 ASP cc_start: 0.8860 (t0) cc_final: 0.8561 (t0) outliers start: 5 outliers final: 3 residues processed: 649 average time/residue: 0.1595 time to fit residues: 152.6786 Evaluate side-chains 473 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 470 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 241 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 231 HIS C 46 GLN D 231 HIS F 77 HIS F 231 HIS I 41 GLN I 46 GLN J 46 GLN K 120 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.109765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080169 restraints weight = 43435.588| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.80 r_work: 0.2885 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20942 Z= 0.133 Angle : 0.607 7.642 28843 Z= 0.336 Chirality : 0.044 0.175 3148 Planarity : 0.004 0.044 3378 Dihedral : 20.373 151.024 3680 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.46 % Favored : 98.50 % Rotamer: Outliers : 1.78 % Allowed : 9.84 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.15), residues: 2327 helix: -3.22 (0.25), residues: 180 sheet: -1.10 (0.14), residues: 1040 loop : -1.49 (0.16), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 145 TYR 0.016 0.001 TYR H 130 PHE 0.009 0.001 PHE C 228 TRP 0.017 0.001 TRP G 110 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00291 (20942) covalent geometry : angle 0.60736 (28843) hydrogen bonds : bond 0.03768 ( 476) hydrogen bonds : angle 5.84921 ( 1299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 546 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8855 (tp-100) REVERT: A 52 MET cc_start: 0.9166 (ptp) cc_final: 0.8856 (ptp) REVERT: A 65 ASN cc_start: 0.8894 (t0) cc_final: 0.8650 (t0) REVERT: A 67 TYR cc_start: 0.8753 (m-80) cc_final: 0.8454 (m-10) REVERT: A 73 GLU cc_start: 0.8195 (pm20) cc_final: 0.7944 (pm20) REVERT: A 120 GLN cc_start: 0.8350 (pt0) cc_final: 0.7563 (tm-30) REVERT: A 164 ASP cc_start: 0.7745 (t0) cc_final: 0.7525 (t0) REVERT: A 175 ASN cc_start: 0.9023 (t0) cc_final: 0.8692 (t0) REVERT: A 189 LYS cc_start: 0.8657 (mmtp) cc_final: 0.8431 (mmtp) REVERT: A 203 VAL cc_start: 0.8391 (t) cc_final: 0.8040 (p) REVERT: A 205 ASP cc_start: 0.8483 (t0) cc_final: 0.7861 (t0) REVERT: B 116 THR cc_start: 0.9046 (t) cc_final: 0.8748 (p) REVERT: B 142 LYS cc_start: 0.9400 (mmtm) cc_final: 0.9189 (mmtm) REVERT: B 146 GLU cc_start: 0.9181 (mp0) cc_final: 0.8873 (pm20) REVERT: B 164 ASP cc_start: 0.8957 (p0) cc_final: 0.8474 (p0) REVERT: B 175 ASN cc_start: 0.9111 (t0) cc_final: 0.8886 (t0) REVERT: C 135 LYS cc_start: 0.9080 (ttpp) cc_final: 0.8616 (tttp) REVERT: C 146 GLU cc_start: 0.8920 (mp0) cc_final: 0.8677 (pm20) REVERT: C 164 ASP cc_start: 0.8891 (p0) cc_final: 0.8496 (p0) REVERT: D 95 ASP cc_start: 0.8392 (t0) cc_final: 0.7979 (t0) REVERT: D 99 CYS cc_start: 0.8980 (m) cc_final: 0.8650 (m) REVERT: D 164 ASP cc_start: 0.9021 (p0) cc_final: 0.8734 (p0) REVERT: D 175 ASN cc_start: 0.9313 (t0) cc_final: 0.9101 (t0) REVERT: E 34 LYS cc_start: 0.7104 (mmtt) cc_final: 0.6530 (mmtp) REVERT: E 46 GLN cc_start: 0.7901 (tp40) cc_final: 0.7602 (tp-100) REVERT: E 62 ASP cc_start: 0.8339 (t0) cc_final: 0.7848 (t0) REVERT: E 72 ASP cc_start: 0.8446 (m-30) cc_final: 0.7954 (m-30) REVERT: E 75 ASN cc_start: 0.8550 (m-40) cc_final: 0.7947 (m-40) REVERT: E 95 ASP cc_start: 0.7467 (t0) cc_final: 0.7020 (t0) REVERT: E 99 CYS cc_start: 0.8551 (m) cc_final: 0.7935 (m) REVERT: E 164 ASP cc_start: 0.8523 (p0) cc_final: 0.8193 (p0) REVERT: F 109 MET cc_start: 0.9254 (ttt) cc_final: 0.9004 (ttt) REVERT: F 132 ASP cc_start: 0.8670 (p0) cc_final: 0.8403 (t0) REVERT: F 135 LYS cc_start: 0.9126 (ttmm) cc_final: 0.8618 (tptt) REVERT: F 164 ASP cc_start: 0.9288 (p0) cc_final: 0.9014 (p0) REVERT: F 217 TYR cc_start: 0.8811 (m-80) cc_final: 0.8589 (m-80) REVERT: G 67 TYR cc_start: 0.8813 (m-80) cc_final: 0.8461 (m-80) REVERT: G 217 TYR cc_start: 0.9073 (m-80) cc_final: 0.8826 (m-80) REVERT: G 218 MET cc_start: 0.8671 (ttp) cc_final: 0.8410 (ttp) REVERT: H 109 MET cc_start: 0.9051 (ttt) cc_final: 0.8820 (ttm) REVERT: H 147 LEU cc_start: 0.9172 (mt) cc_final: 0.8969 (mp) REVERT: H 154 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8550 (mtpt) REVERT: H 164 ASP cc_start: 0.8543 (p0) cc_final: 0.8233 (p0) REVERT: H 201 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7338 (mtmm) REVERT: H 239 LYS cc_start: 0.7561 (ptmt) cc_final: 0.7253 (ptmm) REVERT: H 241 VAL cc_start: 0.8524 (p) cc_final: 0.8274 (m) REVERT: I 43 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8045 (tm-30) REVERT: I 62 ASP cc_start: 0.8403 (t70) cc_final: 0.8104 (t0) REVERT: I 75 ASN cc_start: 0.7694 (m-40) cc_final: 0.7488 (m-40) REVERT: I 161 MET cc_start: 0.8829 (mtm) cc_final: 0.8378 (mpp) REVERT: I 164 ASP cc_start: 0.8514 (p0) cc_final: 0.8243 (p0) REVERT: J 41 GLN cc_start: 0.8370 (mt0) cc_final: 0.7969 (mt0) REVERT: J 103 ASN cc_start: 0.9080 (p0) cc_final: 0.8820 (p0) REVERT: J 164 ASP cc_start: 0.8950 (p0) cc_final: 0.8512 (p0) REVERT: J 205 ASP cc_start: 0.8261 (t0) cc_final: 0.7818 (t0) REVERT: K 101 TYR cc_start: 0.7991 (m-80) cc_final: 0.7717 (m-80) REVERT: K 164 ASP cc_start: 0.8909 (p0) cc_final: 0.8638 (p0) REVERT: K 199 GLN cc_start: 0.8324 (mt0) cc_final: 0.8006 (mp10) REVERT: K 205 ASP cc_start: 0.8689 (t0) cc_final: 0.8341 (t0) outliers start: 34 outliers final: 23 residues processed: 558 average time/residue: 0.1330 time to fit residues: 116.9773 Evaluate side-chains 495 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 472 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 178 TRP Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 99 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 227 optimal weight: 0.0070 chunk 90 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 202 ASN H 75 ASN J 224 ASN K 231 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.107916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.077994 restraints weight = 43992.752| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.83 r_work: 0.2926 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20942 Z= 0.157 Angle : 0.573 7.616 28843 Z= 0.314 Chirality : 0.042 0.140 3148 Planarity : 0.004 0.074 3378 Dihedral : 20.437 150.296 3678 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.15 % Rotamer: Outliers : 2.35 % Allowed : 14.44 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.15), residues: 2327 helix: -2.57 (0.27), residues: 198 sheet: -0.46 (0.15), residues: 1016 loop : -1.45 (0.16), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 183 TYR 0.017 0.001 TYR C 113 PHE 0.016 0.002 PHE F 128 TRP 0.018 0.001 TRP E 110 HIS 0.004 0.001 HIS F 91 Details of bonding type rmsd covalent geometry : bond 0.00361 (20942) covalent geometry : angle 0.57254 (28843) hydrogen bonds : bond 0.03638 ( 476) hydrogen bonds : angle 5.34560 ( 1299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 483 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8798 (tp-100) REVERT: A 52 MET cc_start: 0.9172 (ptp) cc_final: 0.8810 (ptp) REVERT: A 65 ASN cc_start: 0.8792 (t0) cc_final: 0.8370 (t0) REVERT: A 67 TYR cc_start: 0.8770 (m-80) cc_final: 0.8387 (m-10) REVERT: A 73 GLU cc_start: 0.8197 (pm20) cc_final: 0.7976 (pm20) REVERT: A 120 GLN cc_start: 0.8383 (pt0) cc_final: 0.7662 (pp30) REVERT: A 175 ASN cc_start: 0.9128 (t0) cc_final: 0.8826 (t0) REVERT: A 203 VAL cc_start: 0.8408 (t) cc_final: 0.8056 (p) REVERT: A 205 ASP cc_start: 0.8483 (t0) cc_final: 0.7883 (t0) REVERT: B 67 TYR cc_start: 0.8900 (m-10) cc_final: 0.8606 (m-10) REVERT: B 95 ASP cc_start: 0.8115 (t0) cc_final: 0.7860 (t0) REVERT: B 164 ASP cc_start: 0.9001 (p0) cc_final: 0.8720 (p0) REVERT: B 175 ASN cc_start: 0.9078 (t0) cc_final: 0.8855 (t0) REVERT: C 135 LYS cc_start: 0.9168 (ttpp) cc_final: 0.8676 (tttp) REVERT: C 164 ASP cc_start: 0.8967 (p0) cc_final: 0.8256 (p0) REVERT: D 95 ASP cc_start: 0.8309 (t0) cc_final: 0.8046 (t0) REVERT: D 164 ASP cc_start: 0.9043 (p0) cc_final: 0.8677 (p0) REVERT: D 175 ASN cc_start: 0.9336 (t0) cc_final: 0.9111 (t0) REVERT: E 34 LYS cc_start: 0.7167 (mmtt) cc_final: 0.6729 (mmtp) REVERT: E 43 GLN cc_start: 0.8646 (tp-100) cc_final: 0.8408 (tp-100) REVERT: E 62 ASP cc_start: 0.8497 (t0) cc_final: 0.7990 (t0) REVERT: E 72 ASP cc_start: 0.8459 (m-30) cc_final: 0.7965 (m-30) REVERT: E 75 ASN cc_start: 0.8458 (m-40) cc_final: 0.7839 (m-40) REVERT: E 95 ASP cc_start: 0.7681 (t0) cc_final: 0.7165 (t0) REVERT: E 99 CYS cc_start: 0.8484 (m) cc_final: 0.7902 (m) REVERT: E 164 ASP cc_start: 0.8532 (p0) cc_final: 0.8161 (p0) REVERT: E 201 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8078 (mtmm) REVERT: E 217 TYR cc_start: 0.8927 (m-80) cc_final: 0.8648 (m-80) REVERT: F 73 GLU cc_start: 0.7796 (tp30) cc_final: 0.7495 (tp30) REVERT: F 109 MET cc_start: 0.9289 (ttt) cc_final: 0.9011 (ttt) REVERT: F 132 ASP cc_start: 0.8721 (p0) cc_final: 0.8424 (t0) REVERT: F 164 ASP cc_start: 0.9284 (p0) cc_final: 0.8936 (p0) REVERT: G 218 MET cc_start: 0.8636 (ttp) cc_final: 0.8372 (ttp) REVERT: H 103 ASN cc_start: 0.9014 (p0) cc_final: 0.8769 (p0) REVERT: H 109 MET cc_start: 0.9065 (ttt) cc_final: 0.8785 (ttm) REVERT: H 135 LYS cc_start: 0.9258 (tttp) cc_final: 0.8788 (tptp) REVERT: H 142 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8661 (mmtt) REVERT: H 164 ASP cc_start: 0.8561 (p0) cc_final: 0.8242 (p0) REVERT: H 201 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7340 (mtmm) REVERT: H 241 VAL cc_start: 0.8732 (p) cc_final: 0.8480 (m) REVERT: I 43 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8090 (tm-30) REVERT: I 62 ASP cc_start: 0.8426 (t70) cc_final: 0.8153 (t0) REVERT: I 75 ASN cc_start: 0.7796 (m-40) cc_final: 0.7575 (m-40) REVERT: I 80 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7357 (mm-30) REVERT: I 161 MET cc_start: 0.8836 (mtm) cc_final: 0.8443 (mpp) REVERT: I 164 ASP cc_start: 0.8457 (p0) cc_final: 0.8191 (p0) REVERT: J 41 GLN cc_start: 0.8164 (mt0) cc_final: 0.7787 (mt0) REVERT: J 103 ASN cc_start: 0.9113 (p0) cc_final: 0.8820 (p0) REVERT: J 164 ASP cc_start: 0.9057 (p0) cc_final: 0.8617 (p0) REVERT: J 205 ASP cc_start: 0.8292 (t0) cc_final: 0.7736 (t0) REVERT: J 224 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8681 (p0) REVERT: K 90 TYR cc_start: 0.9524 (m-80) cc_final: 0.9310 (m-10) REVERT: K 95 ASP cc_start: 0.7956 (t0) cc_final: 0.7723 (t0) REVERT: K 164 ASP cc_start: 0.8930 (p0) cc_final: 0.8630 (p0) REVERT: K 199 GLN cc_start: 0.8079 (mt0) cc_final: 0.7749 (mp10) REVERT: K 205 ASP cc_start: 0.8669 (t0) cc_final: 0.8306 (t0) outliers start: 45 outliers final: 32 residues processed: 506 average time/residue: 0.1353 time to fit residues: 107.9881 Evaluate side-chains 478 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 445 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 99 CYS Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 239 LYS Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 178 TRP Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 224 ASN Chi-restraints excluded: chain K residue 99 CYS Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 211 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 168 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN G 243 ASN H 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.107295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.077261 restraints weight = 43637.201| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.84 r_work: 0.2919 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20942 Z= 0.156 Angle : 0.553 6.998 28843 Z= 0.302 Chirality : 0.042 0.179 3148 Planarity : 0.004 0.054 3378 Dihedral : 20.404 157.988 3678 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.68 % Favored : 98.28 % Rotamer: Outliers : 2.41 % Allowed : 15.49 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.16), residues: 2327 helix: -2.28 (0.29), residues: 198 sheet: -0.16 (0.15), residues: 1016 loop : -1.41 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 150 TYR 0.019 0.001 TYR C 113 PHE 0.015 0.001 PHE G 128 TRP 0.016 0.001 TRP G 110 HIS 0.004 0.001 HIS K 231 Details of bonding type rmsd covalent geometry : bond 0.00362 (20942) covalent geometry : angle 0.55341 (28843) hydrogen bonds : bond 0.03258 ( 476) hydrogen bonds : angle 5.18195 ( 1299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 473 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.9157 (ptp) cc_final: 0.8873 (ptp) REVERT: A 65 ASN cc_start: 0.8890 (t0) cc_final: 0.8606 (t0) REVERT: A 73 GLU cc_start: 0.8237 (pm20) cc_final: 0.7950 (pm20) REVERT: A 120 GLN cc_start: 0.8420 (pt0) cc_final: 0.7684 (pp30) REVERT: A 175 ASN cc_start: 0.9213 (t0) cc_final: 0.8941 (t0) REVERT: A 182 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8442 (mptt) REVERT: A 203 VAL cc_start: 0.8517 (t) cc_final: 0.8170 (p) REVERT: A 205 ASP cc_start: 0.8493 (t0) cc_final: 0.7877 (t0) REVERT: B 67 TYR cc_start: 0.8993 (m-10) cc_final: 0.8640 (m-10) REVERT: B 164 ASP cc_start: 0.8989 (p0) cc_final: 0.8688 (p0) REVERT: B 175 ASN cc_start: 0.9057 (t0) cc_final: 0.8854 (t0) REVERT: C 135 LYS cc_start: 0.9218 (ttpp) cc_final: 0.8796 (tttp) REVERT: C 164 ASP cc_start: 0.9012 (p0) cc_final: 0.8283 (p0) REVERT: D 95 ASP cc_start: 0.8223 (t70) cc_final: 0.7936 (t0) REVERT: D 164 ASP cc_start: 0.8998 (p0) cc_final: 0.8607 (p0) REVERT: D 175 ASN cc_start: 0.9345 (t0) cc_final: 0.9107 (t0) REVERT: E 34 LYS cc_start: 0.7173 (mmtt) cc_final: 0.6670 (mmtp) REVERT: E 62 ASP cc_start: 0.8503 (t0) cc_final: 0.7985 (t0) REVERT: E 75 ASN cc_start: 0.8491 (m-40) cc_final: 0.8065 (m-40) REVERT: E 95 ASP cc_start: 0.7867 (t0) cc_final: 0.7315 (t0) REVERT: E 99 CYS cc_start: 0.8575 (m) cc_final: 0.7984 (m) REVERT: E 164 ASP cc_start: 0.8528 (p0) cc_final: 0.8128 (p0) REVERT: E 201 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8108 (mtmm) REVERT: F 73 GLU cc_start: 0.7828 (tp30) cc_final: 0.7460 (tp30) REVERT: F 109 MET cc_start: 0.9270 (ttt) cc_final: 0.8979 (ttt) REVERT: F 132 ASP cc_start: 0.8679 (p0) cc_final: 0.8387 (t0) REVERT: F 135 LYS cc_start: 0.9130 (ttmm) cc_final: 0.8579 (tptt) REVERT: F 164 ASP cc_start: 0.9230 (p0) cc_final: 0.8796 (p0) REVERT: F 205 ASP cc_start: 0.8570 (t0) cc_final: 0.8350 (t0) REVERT: G 67 TYR cc_start: 0.9036 (m-80) cc_final: 0.8556 (m-80) REVERT: G 218 MET cc_start: 0.8693 (ttp) cc_final: 0.8295 (ttp) REVERT: H 103 ASN cc_start: 0.9028 (p0) cc_final: 0.8765 (p0) REVERT: H 109 MET cc_start: 0.9063 (ttt) cc_final: 0.8778 (ttm) REVERT: H 135 LYS cc_start: 0.9190 (tttp) cc_final: 0.8798 (tptp) REVERT: H 164 ASP cc_start: 0.8594 (p0) cc_final: 0.8259 (p0) REVERT: H 179 LYS cc_start: 0.4743 (tttt) cc_final: 0.4098 (tttt) REVERT: H 201 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7376 (mtmm) REVERT: H 241 VAL cc_start: 0.8684 (p) cc_final: 0.8448 (m) REVERT: I 43 GLN cc_start: 0.8565 (tp-100) cc_final: 0.8172 (tm-30) REVERT: I 62 ASP cc_start: 0.8472 (t70) cc_final: 0.7904 (t0) REVERT: I 75 ASN cc_start: 0.7912 (m-40) cc_final: 0.7671 (m-40) REVERT: I 161 MET cc_start: 0.8881 (mtm) cc_final: 0.8528 (mpp) REVERT: I 164 ASP cc_start: 0.8484 (p0) cc_final: 0.8224 (p0) REVERT: J 41 GLN cc_start: 0.8184 (mt0) cc_final: 0.7807 (mt0) REVERT: J 103 ASN cc_start: 0.9130 (p0) cc_final: 0.8894 (p0) REVERT: J 164 ASP cc_start: 0.9088 (p0) cc_final: 0.8623 (p0) REVERT: K 146 GLU cc_start: 0.9001 (pp20) cc_final: 0.8783 (pp20) REVERT: K 164 ASP cc_start: 0.8956 (p0) cc_final: 0.8680 (p0) REVERT: K 199 GLN cc_start: 0.7861 (mt0) cc_final: 0.7524 (mp10) REVERT: K 205 ASP cc_start: 0.8671 (t0) cc_final: 0.8295 (t0) outliers start: 46 outliers final: 34 residues processed: 496 average time/residue: 0.1370 time to fit residues: 107.5479 Evaluate side-chains 489 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 455 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain G residue 99 CYS Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 239 LYS Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 178 TRP Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 99 CYS Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 211 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 140 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 21 optimal weight: 0.0010 chunk 182 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 4 optimal weight: 0.0040 chunk 217 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 10 optimal weight: 0.0060 chunk 38 optimal weight: 7.9990 chunk 193 optimal weight: 20.0000 overall best weight: 1.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 233 GLN H 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.108729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.078777 restraints weight = 43365.138| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.82 r_work: 0.2941 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20942 Z= 0.115 Angle : 0.524 7.304 28843 Z= 0.285 Chirality : 0.041 0.153 3148 Planarity : 0.004 0.052 3378 Dihedral : 20.322 164.137 3678 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.67 % Allowed : 16.06 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.16), residues: 2327 helix: -1.93 (0.32), residues: 198 sheet: 0.14 (0.15), residues: 1013 loop : -1.37 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 183 TYR 0.018 0.001 TYR C 113 PHE 0.015 0.001 PHE F 128 TRP 0.019 0.001 TRP J 110 HIS 0.003 0.001 HIS G 47 Details of bonding type rmsd covalent geometry : bond 0.00265 (20942) covalent geometry : angle 0.52414 (28843) hydrogen bonds : bond 0.02717 ( 476) hydrogen bonds : angle 4.92699 ( 1299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 480 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.9127 (ptp) cc_final: 0.8808 (ptp) REVERT: A 65 ASN cc_start: 0.8717 (t0) cc_final: 0.7882 (t0) REVERT: A 67 TYR cc_start: 0.8703 (m-10) cc_final: 0.7823 (m-10) REVERT: A 73 GLU cc_start: 0.8341 (pm20) cc_final: 0.8084 (pm20) REVERT: A 120 GLN cc_start: 0.8461 (pt0) cc_final: 0.7777 (pp30) REVERT: A 175 ASN cc_start: 0.9235 (t0) cc_final: 0.8970 (t0) REVERT: A 182 LYS cc_start: 0.8944 (mtpp) cc_final: 0.8417 (mptt) REVERT: A 203 VAL cc_start: 0.8474 (t) cc_final: 0.8092 (p) REVERT: A 205 ASP cc_start: 0.8488 (t0) cc_final: 0.7780 (t0) REVERT: B 67 TYR cc_start: 0.8945 (m-10) cc_final: 0.8494 (m-10) REVERT: B 95 ASP cc_start: 0.8026 (t0) cc_final: 0.7766 (t0) REVERT: B 146 GLU cc_start: 0.9234 (mp0) cc_final: 0.8969 (pm20) REVERT: B 164 ASP cc_start: 0.8985 (p0) cc_final: 0.8667 (p0) REVERT: B 175 ASN cc_start: 0.9037 (t0) cc_final: 0.8830 (t0) REVERT: C 67 TYR cc_start: 0.9024 (m-80) cc_final: 0.8785 (m-80) REVERT: C 164 ASP cc_start: 0.8921 (p0) cc_final: 0.8174 (p0) REVERT: D 95 ASP cc_start: 0.8296 (t70) cc_final: 0.8003 (t0) REVERT: D 164 ASP cc_start: 0.8984 (p0) cc_final: 0.8606 (p0) REVERT: D 175 ASN cc_start: 0.9342 (t0) cc_final: 0.9122 (t0) REVERT: D 189 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8546 (mmtp) REVERT: D 192 SER cc_start: 0.8382 (p) cc_final: 0.8101 (p) REVERT: E 34 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6665 (mmtp) REVERT: E 62 ASP cc_start: 0.8504 (t0) cc_final: 0.7967 (t0) REVERT: E 75 ASN cc_start: 0.8504 (m-40) cc_final: 0.8061 (m110) REVERT: E 95 ASP cc_start: 0.7986 (t0) cc_final: 0.7419 (t0) REVERT: E 99 CYS cc_start: 0.8609 (m) cc_final: 0.8008 (m) REVERT: E 164 ASP cc_start: 0.8523 (p0) cc_final: 0.8104 (p0) REVERT: E 201 LYS cc_start: 0.8587 (mtmt) cc_final: 0.7926 (mtmm) REVERT: F 109 MET cc_start: 0.9247 (ttt) cc_final: 0.8987 (ttt) REVERT: F 132 ASP cc_start: 0.8667 (p0) cc_final: 0.8322 (t0) REVERT: F 135 LYS cc_start: 0.9134 (ttmm) cc_final: 0.8625 (tptt) REVERT: F 164 ASP cc_start: 0.9234 (p0) cc_final: 0.8800 (p0) REVERT: F 205 ASP cc_start: 0.8484 (t0) cc_final: 0.8202 (t0) REVERT: G 67 TYR cc_start: 0.8953 (m-80) cc_final: 0.8677 (m-80) REVERT: G 109 MET cc_start: 0.9300 (ttt) cc_final: 0.8987 (tpp) REVERT: G 197 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8559 (ttm-80) REVERT: G 218 MET cc_start: 0.8640 (ttp) cc_final: 0.8360 (ttp) REVERT: H 52 MET cc_start: 0.9009 (ptp) cc_final: 0.8778 (ptp) REVERT: H 75 ASN cc_start: 0.8008 (m110) cc_final: 0.7775 (m-40) REVERT: H 103 ASN cc_start: 0.9048 (p0) cc_final: 0.8816 (p0) REVERT: H 164 ASP cc_start: 0.8581 (p0) cc_final: 0.8275 (p0) REVERT: H 179 LYS cc_start: 0.4705 (tttt) cc_final: 0.4167 (tttp) REVERT: H 201 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7411 (mtmm) REVERT: H 241 VAL cc_start: 0.8719 (p) cc_final: 0.8487 (m) REVERT: I 43 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8225 (tm-30) REVERT: I 62 ASP cc_start: 0.8511 (t70) cc_final: 0.7940 (t0) REVERT: I 75 ASN cc_start: 0.7985 (m-40) cc_final: 0.7705 (m-40) REVERT: I 120 GLN cc_start: 0.9389 (mm-40) cc_final: 0.9127 (mm110) REVERT: I 161 MET cc_start: 0.8769 (mtm) cc_final: 0.8478 (mpp) REVERT: I 164 ASP cc_start: 0.8473 (p0) cc_final: 0.8214 (p0) REVERT: J 41 GLN cc_start: 0.8151 (mt0) cc_final: 0.7769 (mt0) REVERT: J 103 ASN cc_start: 0.9113 (p0) cc_final: 0.8905 (p0) REVERT: J 164 ASP cc_start: 0.9090 (p0) cc_final: 0.8672 (p0) REVERT: K 90 TYR cc_start: 0.9492 (m-80) cc_final: 0.9278 (m-10) REVERT: K 146 GLU cc_start: 0.9052 (pp20) cc_final: 0.8829 (pp20) REVERT: K 164 ASP cc_start: 0.8897 (p0) cc_final: 0.8607 (p0) REVERT: K 199 GLN cc_start: 0.7801 (mt0) cc_final: 0.7501 (mp10) REVERT: K 205 ASP cc_start: 0.8676 (t0) cc_final: 0.8278 (t0) outliers start: 51 outliers final: 38 residues processed: 509 average time/residue: 0.1320 time to fit residues: 106.6609 Evaluate side-chains 492 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 454 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 99 CYS Chi-restraints excluded: chain G residue 239 LYS Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 178 TRP Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 233 GLN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 99 CYS Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 211 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 114 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 213 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 229 optimal weight: 0.0970 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS E 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.108010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.078361 restraints weight = 42753.173| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.76 r_work: 0.2932 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20942 Z= 0.122 Angle : 0.523 7.456 28843 Z= 0.284 Chirality : 0.040 0.145 3148 Planarity : 0.004 0.061 3378 Dihedral : 20.256 168.752 3678 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.72 % Allowed : 16.95 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.16), residues: 2327 helix: -1.77 (0.32), residues: 198 sheet: 0.28 (0.16), residues: 1013 loop : -1.35 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 145 TYR 0.018 0.001 TYR E 90 PHE 0.012 0.001 PHE H 128 TRP 0.014 0.001 TRP E 110 HIS 0.003 0.001 HIS G 47 Details of bonding type rmsd covalent geometry : bond 0.00283 (20942) covalent geometry : angle 0.52286 (28843) hydrogen bonds : bond 0.02674 ( 476) hydrogen bonds : angle 4.84689 ( 1299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 457 time to evaluate : 0.775 Fit side-chains REVERT: A 73 GLU cc_start: 0.8344 (pm20) cc_final: 0.8075 (pm20) REVERT: A 120 GLN cc_start: 0.8502 (pt0) cc_final: 0.7821 (pp30) REVERT: A 175 ASN cc_start: 0.9239 (t0) cc_final: 0.8978 (t0) REVERT: A 182 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8390 (mptt) REVERT: A 203 VAL cc_start: 0.8504 (t) cc_final: 0.8114 (p) REVERT: A 205 ASP cc_start: 0.8480 (t0) cc_final: 0.7772 (t0) REVERT: B 67 TYR cc_start: 0.8953 (m-10) cc_final: 0.8547 (m-10) REVERT: B 164 ASP cc_start: 0.8977 (p0) cc_final: 0.8649 (p0) REVERT: B 175 ASN cc_start: 0.9025 (t0) cc_final: 0.8822 (t0) REVERT: C 67 TYR cc_start: 0.9041 (m-80) cc_final: 0.8821 (m-80) REVERT: C 164 ASP cc_start: 0.8932 (p0) cc_final: 0.8174 (p0) REVERT: D 95 ASP cc_start: 0.8299 (t70) cc_final: 0.8002 (t0) REVERT: D 164 ASP cc_start: 0.8990 (p0) cc_final: 0.8657 (p0) REVERT: D 175 ASN cc_start: 0.9302 (t0) cc_final: 0.9083 (t0) REVERT: D 189 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8642 (mmtt) REVERT: D 192 SER cc_start: 0.8350 (p) cc_final: 0.8052 (p) REVERT: E 34 LYS cc_start: 0.7120 (mmtt) cc_final: 0.6602 (mmtp) REVERT: E 62 ASP cc_start: 0.8500 (t0) cc_final: 0.7957 (t0) REVERT: E 75 ASN cc_start: 0.8501 (m-40) cc_final: 0.8074 (m110) REVERT: E 95 ASP cc_start: 0.7975 (t0) cc_final: 0.7370 (t0) REVERT: E 99 CYS cc_start: 0.8597 (m) cc_final: 0.7991 (m) REVERT: E 164 ASP cc_start: 0.8520 (p0) cc_final: 0.8099 (p0) REVERT: E 201 LYS cc_start: 0.8572 (mtmt) cc_final: 0.7935 (mtmm) REVERT: F 73 GLU cc_start: 0.7896 (tp30) cc_final: 0.7569 (tp30) REVERT: F 109 MET cc_start: 0.9192 (ttt) cc_final: 0.8938 (ttt) REVERT: F 132 ASP cc_start: 0.8673 (p0) cc_final: 0.8326 (t0) REVERT: F 135 LYS cc_start: 0.9131 (ttmm) cc_final: 0.8607 (tptt) REVERT: F 164 ASP cc_start: 0.9247 (p0) cc_final: 0.8826 (p0) REVERT: F 205 ASP cc_start: 0.8446 (t0) cc_final: 0.8115 (t0) REVERT: G 67 TYR cc_start: 0.8948 (m-80) cc_final: 0.8659 (m-80) REVERT: G 197 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8587 (ttm-80) REVERT: G 218 MET cc_start: 0.8691 (ttp) cc_final: 0.8325 (ttp) REVERT: H 103 ASN cc_start: 0.9033 (p0) cc_final: 0.8810 (p0) REVERT: H 135 LYS cc_start: 0.9115 (tttm) cc_final: 0.8729 (tptp) REVERT: H 146 GLU cc_start: 0.9148 (mp0) cc_final: 0.8845 (mp0) REVERT: H 154 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8554 (mtpt) REVERT: H 164 ASP cc_start: 0.8589 (p0) cc_final: 0.8281 (p0) REVERT: H 179 LYS cc_start: 0.4879 (tttt) cc_final: 0.4357 (tttp) REVERT: H 201 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7369 (mtmm) REVERT: H 241 VAL cc_start: 0.8728 (p) cc_final: 0.8505 (m) REVERT: I 43 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8169 (tm-30) REVERT: I 62 ASP cc_start: 0.8505 (t70) cc_final: 0.7914 (t0) REVERT: I 75 ASN cc_start: 0.7865 (m-40) cc_final: 0.7578 (m-40) REVERT: I 100 ARG cc_start: 0.9177 (mmm160) cc_final: 0.8724 (mmm160) REVERT: I 120 GLN cc_start: 0.9386 (mm-40) cc_final: 0.9131 (mm110) REVERT: I 161 MET cc_start: 0.8819 (mtm) cc_final: 0.8476 (mpp) REVERT: I 164 ASP cc_start: 0.8419 (p0) cc_final: 0.8171 (p0) REVERT: J 41 GLN cc_start: 0.8106 (mt0) cc_final: 0.7690 (mt0) REVERT: J 164 ASP cc_start: 0.9104 (p0) cc_final: 0.8695 (p0) REVERT: K 90 TYR cc_start: 0.9457 (m-80) cc_final: 0.9251 (m-10) REVERT: K 164 ASP cc_start: 0.8896 (p0) cc_final: 0.8620 (p0) REVERT: K 199 GLN cc_start: 0.7739 (mt0) cc_final: 0.7439 (mp10) REVERT: K 205 ASP cc_start: 0.8640 (t0) cc_final: 0.8224 (t0) outliers start: 52 outliers final: 42 residues processed: 486 average time/residue: 0.1345 time to fit residues: 103.5403 Evaluate side-chains 491 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 449 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 99 CYS Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 99 CYS Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 211 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 77 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 149 HIS J 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.103014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072951 restraints weight = 43847.635| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.90 r_work: 0.2727 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20942 Z= 0.273 Angle : 0.619 7.428 28843 Z= 0.338 Chirality : 0.042 0.144 3148 Planarity : 0.004 0.060 3378 Dihedral : 20.417 171.794 3678 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.82 % Allowed : 16.48 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.16), residues: 2327 helix: -2.14 (0.32), residues: 168 sheet: 0.07 (0.16), residues: 993 loop : -1.40 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 145 TYR 0.021 0.002 TYR C 113 PHE 0.015 0.002 PHE G 128 TRP 0.022 0.002 TRP I 178 HIS 0.004 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00632 (20942) covalent geometry : angle 0.61867 (28843) hydrogen bonds : bond 0.03934 ( 476) hydrogen bonds : angle 5.35722 ( 1299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 450 time to evaluate : 0.784 Fit side-chains REVERT: A 73 GLU cc_start: 0.8348 (pm20) cc_final: 0.7937 (pm20) REVERT: A 120 GLN cc_start: 0.8538 (pt0) cc_final: 0.7873 (pp30) REVERT: A 175 ASN cc_start: 0.9281 (t0) cc_final: 0.9040 (t0) REVERT: A 182 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8330 (mptt) REVERT: A 203 VAL cc_start: 0.8576 (t) cc_final: 0.8190 (p) REVERT: A 205 ASP cc_start: 0.8570 (t0) cc_final: 0.8183 (t0) REVERT: B 67 TYR cc_start: 0.9193 (m-10) cc_final: 0.8771 (m-10) REVERT: B 164 ASP cc_start: 0.9034 (p0) cc_final: 0.8710 (p0) REVERT: C 164 ASP cc_start: 0.8967 (p0) cc_final: 0.8228 (p0) REVERT: C 205 ASP cc_start: 0.7950 (t0) cc_final: 0.7593 (m-30) REVERT: D 95 ASP cc_start: 0.8308 (t70) cc_final: 0.8006 (t0) REVERT: D 164 ASP cc_start: 0.8986 (p0) cc_final: 0.8776 (p0) REVERT: D 192 SER cc_start: 0.8298 (p) cc_final: 0.7956 (p) REVERT: D 205 ASP cc_start: 0.8559 (t0) cc_final: 0.8138 (t0) REVERT: D 218 MET cc_start: 0.8348 (ttp) cc_final: 0.8114 (ttp) REVERT: E 34 LYS cc_start: 0.7021 (mmtt) cc_final: 0.6637 (mmtp) REVERT: E 62 ASP cc_start: 0.8494 (t0) cc_final: 0.8003 (t0) REVERT: E 75 ASN cc_start: 0.8541 (m-40) cc_final: 0.8128 (m-40) REVERT: E 95 ASP cc_start: 0.7958 (t0) cc_final: 0.7329 (t0) REVERT: E 99 CYS cc_start: 0.8589 (m) cc_final: 0.8016 (m) REVERT: E 164 ASP cc_start: 0.8570 (p0) cc_final: 0.8140 (p0) REVERT: E 201 LYS cc_start: 0.8587 (mtmt) cc_final: 0.7945 (mtmm) REVERT: E 217 TYR cc_start: 0.8810 (m-80) cc_final: 0.8393 (m-80) REVERT: F 109 MET cc_start: 0.9148 (ttt) cc_final: 0.8873 (ttt) REVERT: F 132 ASP cc_start: 0.8692 (p0) cc_final: 0.8412 (t0) REVERT: F 135 LYS cc_start: 0.9130 (ttmm) cc_final: 0.8896 (tppt) REVERT: F 164 ASP cc_start: 0.9286 (p0) cc_final: 0.8894 (p0) REVERT: F 205 ASP cc_start: 0.8578 (t0) cc_final: 0.8219 (t0) REVERT: G 218 MET cc_start: 0.8617 (ttp) cc_final: 0.8259 (ttp) REVERT: H 41 GLN cc_start: 0.7718 (mp10) cc_final: 0.7220 (mp10) REVERT: H 146 GLU cc_start: 0.9161 (mp0) cc_final: 0.8840 (mp0) REVERT: H 164 ASP cc_start: 0.8701 (p0) cc_final: 0.8354 (p0) REVERT: H 201 LYS cc_start: 0.7795 (mtpp) cc_final: 0.7135 (mtmm) REVERT: I 43 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8059 (tm-30) REVERT: I 62 ASP cc_start: 0.8425 (t70) cc_final: 0.7833 (t0) REVERT: I 75 ASN cc_start: 0.7737 (m-40) cc_final: 0.7444 (m-40) REVERT: I 100 ARG cc_start: 0.9180 (mmm160) cc_final: 0.8959 (mmm160) REVERT: I 120 GLN cc_start: 0.9403 (mm-40) cc_final: 0.9172 (mm110) REVERT: I 161 MET cc_start: 0.8950 (mtm) cc_final: 0.8631 (mpp) REVERT: I 164 ASP cc_start: 0.8495 (p0) cc_final: 0.8222 (p0) REVERT: I 192 SER cc_start: 0.8993 (p) cc_final: 0.8729 (p) REVERT: I 199 GLN cc_start: 0.7064 (mt0) cc_final: 0.6782 (mm-40) REVERT: J 43 GLN cc_start: 0.8371 (tp-100) cc_final: 0.8152 (tp-100) REVERT: J 164 ASP cc_start: 0.9168 (p0) cc_final: 0.8777 (p0) REVERT: J 205 ASP cc_start: 0.8249 (t0) cc_final: 0.7619 (t0) REVERT: K 43 GLN cc_start: 0.8753 (tp40) cc_final: 0.8262 (tp-100) REVERT: K 164 ASP cc_start: 0.8884 (p0) cc_final: 0.8657 (p0) REVERT: K 199 GLN cc_start: 0.8020 (mt0) cc_final: 0.7679 (mp10) REVERT: K 205 ASP cc_start: 0.8815 (t0) cc_final: 0.8426 (t0) outliers start: 73 outliers final: 61 residues processed: 491 average time/residue: 0.1309 time to fit residues: 102.3904 Evaluate side-chains 490 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 429 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 99 CYS Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 239 LYS Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 80 GLU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 185 ILE Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 233 GLN Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 185 ILE Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 99 CYS Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 211 ILE Chi-restraints excluded: chain K residue 236 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 223 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS E 202 ASN G 233 GLN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN I 125 GLN J 46 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.105582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.075768 restraints weight = 43455.554| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.78 r_work: 0.2883 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20942 Z= 0.157 Angle : 0.563 7.322 28843 Z= 0.307 Chirality : 0.041 0.146 3148 Planarity : 0.004 0.053 3378 Dihedral : 20.316 174.195 3678 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.30 % Allowed : 17.95 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.16), residues: 2327 helix: -1.89 (0.34), residues: 186 sheet: 0.14 (0.16), residues: 990 loop : -1.42 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 183 TYR 0.018 0.001 TYR C 113 PHE 0.013 0.001 PHE H 128 TRP 0.016 0.001 TRP C 110 HIS 0.004 0.001 HIS G 47 Details of bonding type rmsd covalent geometry : bond 0.00365 (20942) covalent geometry : angle 0.56349 (28843) hydrogen bonds : bond 0.03087 ( 476) hydrogen bonds : angle 5.09330 ( 1299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 445 time to evaluate : 0.786 Fit side-chains REVERT: A 73 GLU cc_start: 0.8381 (pm20) cc_final: 0.8020 (pm20) REVERT: A 120 GLN cc_start: 0.8479 (pt0) cc_final: 0.7826 (pp30) REVERT: A 175 ASN cc_start: 0.9298 (t0) cc_final: 0.9044 (t0) REVERT: A 182 LYS cc_start: 0.8983 (mtpp) cc_final: 0.8445 (mptt) REVERT: A 203 VAL cc_start: 0.8580 (t) cc_final: 0.8178 (p) REVERT: A 205 ASP cc_start: 0.8610 (t0) cc_final: 0.8185 (t0) REVERT: B 67 TYR cc_start: 0.9128 (m-10) cc_final: 0.8755 (m-10) REVERT: B 164 ASP cc_start: 0.9010 (p0) cc_final: 0.8691 (p0) REVERT: C 164 ASP cc_start: 0.8989 (p0) cc_final: 0.8267 (p0) REVERT: C 205 ASP cc_start: 0.8073 (t0) cc_final: 0.7743 (m-30) REVERT: D 95 ASP cc_start: 0.8463 (t70) cc_final: 0.8015 (t0) REVERT: D 205 ASP cc_start: 0.8527 (t0) cc_final: 0.8099 (t0) REVERT: E 34 LYS cc_start: 0.7206 (mmtt) cc_final: 0.6861 (mmtp) REVERT: E 62 ASP cc_start: 0.8543 (t0) cc_final: 0.8029 (t0) REVERT: E 75 ASN cc_start: 0.8626 (m-40) cc_final: 0.8404 (m110) REVERT: E 95 ASP cc_start: 0.8091 (t0) cc_final: 0.7457 (t0) REVERT: E 99 CYS cc_start: 0.8796 (m) cc_final: 0.8304 (m) REVERT: E 164 ASP cc_start: 0.8623 (p0) cc_final: 0.8188 (p0) REVERT: E 201 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8114 (mtmm) REVERT: E 217 TYR cc_start: 0.8906 (m-80) cc_final: 0.8633 (m-80) REVERT: F 109 MET cc_start: 0.9190 (ttt) cc_final: 0.8906 (ttt) REVERT: F 132 ASP cc_start: 0.8690 (p0) cc_final: 0.8438 (t0) REVERT: F 135 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8608 (tptt) REVERT: F 164 ASP cc_start: 0.9278 (p0) cc_final: 0.8859 (p0) REVERT: F 205 ASP cc_start: 0.8526 (t0) cc_final: 0.8110 (t0) REVERT: G 197 ARG cc_start: 0.9103 (ttp80) cc_final: 0.8538 (ttm-80) REVERT: G 218 MET cc_start: 0.8716 (ttp) cc_final: 0.8350 (ttp) REVERT: H 135 LYS cc_start: 0.9134 (tttm) cc_final: 0.8708 (tptp) REVERT: H 146 GLU cc_start: 0.9097 (mp0) cc_final: 0.8697 (mp0) REVERT: H 154 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8601 (mtpt) REVERT: H 164 ASP cc_start: 0.8680 (p0) cc_final: 0.8349 (p0) REVERT: H 201 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7343 (mtmm) REVERT: I 43 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8159 (tm-30) REVERT: I 62 ASP cc_start: 0.8514 (t70) cc_final: 0.7920 (t0) REVERT: I 75 ASN cc_start: 0.7824 (m-40) cc_final: 0.7498 (m-40) REVERT: I 100 ARG cc_start: 0.9166 (mmm160) cc_final: 0.8929 (mmm160) REVERT: I 120 GLN cc_start: 0.9390 (mm-40) cc_final: 0.9153 (mm110) REVERT: I 154 LYS cc_start: 0.8765 (mttm) cc_final: 0.8556 (mttm) REVERT: I 161 MET cc_start: 0.8881 (mtm) cc_final: 0.8365 (mpp) REVERT: I 164 ASP cc_start: 0.8491 (p0) cc_final: 0.8222 (p0) REVERT: I 192 SER cc_start: 0.8917 (p) cc_final: 0.8635 (p) REVERT: J 41 GLN cc_start: 0.8162 (mt0) cc_final: 0.7856 (mt0) REVERT: J 43 GLN cc_start: 0.8483 (tp-100) cc_final: 0.8251 (tp-100) REVERT: J 164 ASP cc_start: 0.9162 (p0) cc_final: 0.8786 (p0) REVERT: K 43 GLN cc_start: 0.8828 (tp40) cc_final: 0.8363 (tp-100) REVERT: K 164 ASP cc_start: 0.8868 (p0) cc_final: 0.8641 (p0) REVERT: K 199 GLN cc_start: 0.7927 (mt0) cc_final: 0.7572 (mp10) REVERT: K 205 ASP cc_start: 0.8803 (t0) cc_final: 0.8422 (t0) outliers start: 63 outliers final: 53 residues processed: 484 average time/residue: 0.1298 time to fit residues: 99.9578 Evaluate side-chains 490 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 437 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 99 CYS Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 239 LYS Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 233 GLN Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 99 CYS Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 211 ILE Chi-restraints excluded: chain K residue 236 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 224 optimal weight: 0.0030 chunk 155 optimal weight: 0.2980 chunk 134 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 170 optimal weight: 0.2980 chunk 97 optimal weight: 9.9990 chunk 150 optimal weight: 0.0970 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.108459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078651 restraints weight = 43143.843| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.81 r_work: 0.2947 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20942 Z= 0.109 Angle : 0.541 7.285 28843 Z= 0.294 Chirality : 0.040 0.145 3148 Planarity : 0.004 0.052 3378 Dihedral : 20.148 176.011 3678 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.72 % Allowed : 18.89 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2327 helix: -1.63 (0.35), residues: 186 sheet: 0.36 (0.16), residues: 1003 loop : -1.33 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 145 TYR 0.015 0.001 TYR C 113 PHE 0.013 0.001 PHE H 187 TRP 0.019 0.001 TRP I 110 HIS 0.003 0.000 HIS G 47 Details of bonding type rmsd covalent geometry : bond 0.00250 (20942) covalent geometry : angle 0.54085 (28843) hydrogen bonds : bond 0.02280 ( 476) hydrogen bonds : angle 4.63060 ( 1299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 458 time to evaluate : 0.639 Fit side-chains REVERT: A 73 GLU cc_start: 0.8379 (pm20) cc_final: 0.8124 (pm20) REVERT: A 120 GLN cc_start: 0.8444 (pt0) cc_final: 0.7870 (pp30) REVERT: A 175 ASN cc_start: 0.9267 (t0) cc_final: 0.9012 (t0) REVERT: A 182 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8417 (mptt) REVERT: A 201 LYS cc_start: 0.8689 (mtpt) cc_final: 0.7962 (mtmm) REVERT: A 203 VAL cc_start: 0.8585 (t) cc_final: 0.8165 (p) REVERT: A 205 ASP cc_start: 0.8596 (t0) cc_final: 0.7913 (t0) REVERT: B 67 TYR cc_start: 0.8979 (m-10) cc_final: 0.8583 (m-10) REVERT: C 164 ASP cc_start: 0.8967 (p0) cc_final: 0.8230 (p0) REVERT: C 205 ASP cc_start: 0.7979 (t0) cc_final: 0.7615 (m-30) REVERT: D 95 ASP cc_start: 0.8397 (t70) cc_final: 0.8136 (t0) REVERT: E 34 LYS cc_start: 0.7097 (mmtt) cc_final: 0.6643 (mmtp) REVERT: E 62 ASP cc_start: 0.8485 (t0) cc_final: 0.7960 (t0) REVERT: E 75 ASN cc_start: 0.8533 (m-40) cc_final: 0.8156 (m110) REVERT: E 95 ASP cc_start: 0.8122 (t0) cc_final: 0.7481 (t0) REVERT: E 99 CYS cc_start: 0.8807 (m) cc_final: 0.8317 (m) REVERT: E 164 ASP cc_start: 0.8571 (p0) cc_final: 0.8129 (p0) REVERT: E 201 LYS cc_start: 0.8574 (mtmt) cc_final: 0.7916 (mtmm) REVERT: F 67 TYR cc_start: 0.8681 (m-10) cc_final: 0.7986 (m-10) REVERT: F 109 MET cc_start: 0.9135 (ttt) cc_final: 0.8900 (ttt) REVERT: F 132 ASP cc_start: 0.8664 (p0) cc_final: 0.8371 (t0) REVERT: F 135 LYS cc_start: 0.9128 (ttmm) cc_final: 0.8815 (tptp) REVERT: F 164 ASP cc_start: 0.9281 (p0) cc_final: 0.8830 (p0) REVERT: F 205 ASP cc_start: 0.8469 (t0) cc_final: 0.8028 (t0) REVERT: F 217 TYR cc_start: 0.8941 (m-80) cc_final: 0.8580 (m-80) REVERT: G 189 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8239 (mmtp) REVERT: G 197 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8530 (ttm-80) REVERT: G 218 MET cc_start: 0.8657 (ttp) cc_final: 0.8289 (ttp) REVERT: H 135 LYS cc_start: 0.9106 (tttm) cc_final: 0.8701 (tptp) REVERT: H 146 GLU cc_start: 0.9031 (mp0) cc_final: 0.8670 (mp0) REVERT: H 154 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8638 (mtpt) REVERT: H 164 ASP cc_start: 0.8603 (p0) cc_final: 0.8274 (p0) REVERT: H 201 LYS cc_start: 0.7910 (mtpp) cc_final: 0.7310 (mtmm) REVERT: I 43 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8157 (tm-30) REVERT: I 62 ASP cc_start: 0.8523 (t70) cc_final: 0.7925 (t0) REVERT: I 75 ASN cc_start: 0.7722 (m-40) cc_final: 0.7372 (m-40) REVERT: I 100 ARG cc_start: 0.9143 (mmm160) cc_final: 0.8903 (mmm160) REVERT: I 120 GLN cc_start: 0.9361 (mm-40) cc_final: 0.9095 (mm110) REVERT: I 161 MET cc_start: 0.8759 (mtm) cc_final: 0.8251 (mpp) REVERT: I 164 ASP cc_start: 0.8407 (p0) cc_final: 0.8140 (p0) REVERT: I 192 SER cc_start: 0.8773 (p) cc_final: 0.8209 (t) REVERT: J 41 GLN cc_start: 0.8125 (mt0) cc_final: 0.7699 (mt0) REVERT: J 43 GLN cc_start: 0.8374 (tp-100) cc_final: 0.8123 (tp-100) REVERT: J 164 ASP cc_start: 0.9129 (p0) cc_final: 0.8711 (p0) REVERT: K 43 GLN cc_start: 0.8775 (tp40) cc_final: 0.8310 (tp-100) REVERT: K 73 GLU cc_start: 0.8301 (pm20) cc_final: 0.8054 (pm20) REVERT: K 164 ASP cc_start: 0.8872 (p0) cc_final: 0.8625 (p0) REVERT: K 199 GLN cc_start: 0.7805 (mt0) cc_final: 0.7501 (mp10) REVERT: K 205 ASP cc_start: 0.8589 (t0) cc_final: 0.8157 (t0) outliers start: 52 outliers final: 46 residues processed: 488 average time/residue: 0.1291 time to fit residues: 100.4369 Evaluate side-chains 494 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 448 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 239 LYS Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 211 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 189 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 41 GLN I 149 HIS J 46 GLN J 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.104163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.074307 restraints weight = 43670.297| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.77 r_work: 0.2855 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20942 Z= 0.248 Angle : 0.627 7.975 28843 Z= 0.341 Chirality : 0.042 0.153 3148 Planarity : 0.004 0.064 3378 Dihedral : 20.231 176.076 3678 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.77 % Allowed : 18.84 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.16), residues: 2327 helix: -1.98 (0.31), residues: 198 sheet: 0.15 (0.16), residues: 994 loop : -1.47 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 155 TYR 0.025 0.002 TYR F 90 PHE 0.015 0.002 PHE G 128 TRP 0.023 0.002 TRP I 178 HIS 0.004 0.001 HIS G 47 Details of bonding type rmsd covalent geometry : bond 0.00576 (20942) covalent geometry : angle 0.62727 (28843) hydrogen bonds : bond 0.03674 ( 476) hydrogen bonds : angle 5.18047 ( 1299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4654 Ramachandran restraints generated. 2327 Oldfield, 0 Emsley, 2327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 426 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8392 (pm20) cc_final: 0.8032 (pm20) REVERT: A 120 GLN cc_start: 0.8482 (pt0) cc_final: 0.7905 (pp30) REVERT: A 175 ASN cc_start: 0.9283 (t0) cc_final: 0.9018 (t0) REVERT: A 182 LYS cc_start: 0.8983 (mtpp) cc_final: 0.8409 (mptt) REVERT: A 203 VAL cc_start: 0.8682 (t) cc_final: 0.8293 (p) REVERT: A 205 ASP cc_start: 0.8660 (t0) cc_final: 0.8234 (t0) REVERT: B 67 TYR cc_start: 0.9204 (m-10) cc_final: 0.8780 (m-10) REVERT: B 164 ASP cc_start: 0.8930 (p0) cc_final: 0.8609 (p0) REVERT: C 142 LYS cc_start: 0.9142 (mmtp) cc_final: 0.8877 (mmmm) REVERT: C 164 ASP cc_start: 0.9022 (p0) cc_final: 0.8329 (p0) REVERT: C 205 ASP cc_start: 0.8124 (t0) cc_final: 0.7773 (m-30) REVERT: D 41 GLN cc_start: 0.8101 (mt0) cc_final: 0.7894 (mt0) REVERT: D 95 ASP cc_start: 0.8482 (t70) cc_final: 0.8212 (t0) REVERT: D 205 ASP cc_start: 0.8550 (t0) cc_final: 0.8141 (t0) REVERT: E 34 LYS cc_start: 0.7244 (mmtt) cc_final: 0.6823 (mmtp) REVERT: E 62 ASP cc_start: 0.8615 (t0) cc_final: 0.8098 (t0) REVERT: E 95 ASP cc_start: 0.8123 (t0) cc_final: 0.7452 (t0) REVERT: E 99 CYS cc_start: 0.8815 (m) cc_final: 0.8319 (m) REVERT: E 164 ASP cc_start: 0.8632 (p0) cc_final: 0.8206 (p0) REVERT: E 201 LYS cc_start: 0.8518 (mtmt) cc_final: 0.7882 (mtmm) REVERT: F 65 ASN cc_start: 0.9204 (t0) cc_final: 0.8971 (t0) REVERT: F 109 MET cc_start: 0.9200 (ttt) cc_final: 0.8916 (ttt) REVERT: F 132 ASP cc_start: 0.8704 (p0) cc_final: 0.8458 (t0) REVERT: F 164 ASP cc_start: 0.9279 (p0) cc_final: 0.8907 (p0) REVERT: F 205 ASP cc_start: 0.8581 (t0) cc_final: 0.8125 (t0) REVERT: G 218 MET cc_start: 0.8708 (ttp) cc_final: 0.8318 (ttp) REVERT: H 41 GLN cc_start: 0.7820 (mp10) cc_final: 0.7445 (mm-40) REVERT: H 135 LYS cc_start: 0.9150 (tttm) cc_final: 0.8742 (tptp) REVERT: H 146 GLU cc_start: 0.9164 (mp0) cc_final: 0.8872 (mp0) REVERT: H 154 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8664 (mtpt) REVERT: H 164 ASP cc_start: 0.8681 (p0) cc_final: 0.8336 (p0) REVERT: H 201 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7395 (mtmm) REVERT: I 43 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8199 (tm-30) REVERT: I 62 ASP cc_start: 0.8497 (t70) cc_final: 0.7947 (t0) REVERT: I 75 ASN cc_start: 0.7844 (m-40) cc_final: 0.7506 (m-40) REVERT: I 100 ARG cc_start: 0.9140 (mmm160) cc_final: 0.8894 (mmm160) REVERT: I 120 GLN cc_start: 0.9387 (mm-40) cc_final: 0.9123 (mm110) REVERT: I 154 LYS cc_start: 0.8706 (mttm) cc_final: 0.8491 (mttm) REVERT: I 161 MET cc_start: 0.8944 (mtm) cc_final: 0.8403 (mpp) REVERT: I 164 ASP cc_start: 0.8507 (p0) cc_final: 0.8255 (p0) REVERT: I 192 SER cc_start: 0.8925 (p) cc_final: 0.8686 (p) REVERT: I 199 GLN cc_start: 0.7226 (mt0) cc_final: 0.6967 (mm-40) REVERT: J 41 GLN cc_start: 0.8171 (mt0) cc_final: 0.7880 (mt0) REVERT: J 43 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8274 (tp-100) REVERT: J 164 ASP cc_start: 0.9161 (p0) cc_final: 0.8807 (p0) REVERT: K 43 GLN cc_start: 0.8787 (tp40) cc_final: 0.8371 (tp-100) REVERT: K 52 MET cc_start: 0.8525 (ttp) cc_final: 0.8172 (ttm) REVERT: K 164 ASP cc_start: 0.8868 (p0) cc_final: 0.8659 (p0) REVERT: K 199 GLN cc_start: 0.8047 (mt0) cc_final: 0.7703 (mp10) REVERT: K 205 ASP cc_start: 0.8834 (t0) cc_final: 0.8443 (t0) outliers start: 53 outliers final: 48 residues processed: 458 average time/residue: 0.1326 time to fit residues: 96.4750 Evaluate side-chains 471 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 423 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 239 LYS Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 202 ASN Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 211 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 177 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 75 ASN J 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.106332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.076514 restraints weight = 43343.045| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.78 r_work: 0.2901 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20942 Z= 0.134 Angle : 0.566 7.300 28843 Z= 0.308 Chirality : 0.041 0.146 3148 Planarity : 0.004 0.063 3378 Dihedral : 20.123 176.622 3678 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.51 % Allowed : 19.31 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2327 helix: -1.79 (0.34), residues: 186 sheet: 0.32 (0.16), residues: 987 loop : -1.39 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 183 TYR 0.017 0.001 TYR C 113 PHE 0.013 0.001 PHE H 128 TRP 0.027 0.001 TRP I 110 HIS 0.003 0.001 HIS G 47 Details of bonding type rmsd covalent geometry : bond 0.00313 (20942) covalent geometry : angle 0.56564 (28843) hydrogen bonds : bond 0.02791 ( 476) hydrogen bonds : angle 4.90579 ( 1299) =============================================================================== Job complete usr+sys time: 5513.26 seconds wall clock time: 95 minutes 8.04 seconds (5708.04 seconds total)