Starting phenix.real_space_refine on Sun Aug 24 18:11:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejl_28186/08_2025/8ejl_28186.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejl_28186/08_2025/8ejl_28186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ejl_28186/08_2025/8ejl_28186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejl_28186/08_2025/8ejl_28186.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ejl_28186/08_2025/8ejl_28186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejl_28186/08_2025/8ejl_28186.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 14220 2.51 5 N 3740 2.21 5 O 4045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22155 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 1450 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 202, 1450 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'GLU:plan': 13, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "M" Number of atoms: 831 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 831 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 8, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "N" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 84 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "Z" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 94 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1437 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 6, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 73 Restraints were copied for chains: B, H, Q, W, C, I, R, X, D, J, S, 0, E, K, T, 1, F, O, U, 2, G, P, V, 3 Time building chain proxies: 3.32, per 1000 atoms: 0.15 Number of scatterers: 22155 At special positions: 0 Unit cell: (177.12, 179.28, 90.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 4045 8.00 N 3740 7.00 C 14220 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: 2.18 Conformation dependent library (CDL) restraints added in 990.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5790 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 0 sheets defined 74.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'L' and resid 16 through 30 Processing helix chain 'L' and resid 35 through 44 Processing helix chain 'L' and resid 48 through 58 removed outlier: 3.740A pdb=" N THR L 58 " --> pdb=" O THR L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 84 Processing helix chain 'L' and resid 100 through 105 removed outlier: 3.670A pdb=" N ALA L 105 " --> pdb=" O GLY L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 125 through 146 removed outlier: 3.608A pdb=" N LYS L 140 " --> pdb=" O LEU L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 153 removed outlier: 3.590A pdb=" N ILE L 153 " --> pdb=" O ILE L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 175 Processing helix chain 'L' and resid 178 through 193 removed outlier: 4.605A pdb=" N LEU L 190 " --> pdb=" O THR L 186 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 206 removed outlier: 3.683A pdb=" N THR L 200 " --> pdb=" O PRO L 196 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE L 201 " --> pdb=" O ASP L 197 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY L 206 " --> pdb=" O LEU L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 218 removed outlier: 3.569A pdb=" N CYS L 218 " --> pdb=" O MET L 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 30 Processing helix chain 'M' and resid 35 through 43 Processing helix chain 'M' and resid 48 through 58 Processing helix chain 'M' and resid 62 through 84 Processing helix chain 'M' and resid 110 through 120 Processing helix chain 'M' and resid 125 through 145 Processing helix chain 'N' and resid 149 through 153 Processing helix chain 'N' and resid 160 through 175 Processing helix chain 'N' and resid 178 through 193 removed outlier: 4.424A pdb=" N LEU N 190 " --> pdb=" O THR N 186 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL N 191 " --> pdb=" O GLU N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 206 removed outlier: 3.539A pdb=" N THR N 200 " --> pdb=" O PRO N 196 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE N 201 " --> pdb=" O ASP N 197 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY N 206 " --> pdb=" O LEU N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.724A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.726A pdb=" N MET A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.567A pdb=" N ASN A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 removed outlier: 3.980A pdb=" N GLY A 61 " --> pdb=" O THR A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 62 through 81 removed outlier: 3.551A pdb=" N MET A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.755A pdb=" N ILE A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.880A pdb=" N ASP A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.553A pdb=" N LYS A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 195 through 206 removed outlier: 4.144A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 removed outlier: 3.739A pdb=" N THR B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.670A pdb=" N ALA B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 146 removed outlier: 3.607A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.590A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.605A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.683A pdb=" N THR B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.569A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.424A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.539A pdb=" N THR D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'G' and resid 16 through 31 removed outlier: 3.725A pdb=" N LEU G 20 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN G 21 " --> pdb=" O PRO G 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU G 29 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 44 removed outlier: 3.726A pdb=" N MET G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.567A pdb=" N ASN G 53 " --> pdb=" O PRO G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 61 removed outlier: 3.980A pdb=" N GLY G 61 " --> pdb=" O THR G 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 58 through 61' Processing helix chain 'G' and resid 62 through 81 removed outlier: 3.551A pdb=" N MET G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 119 Processing helix chain 'G' and resid 125 through 146 removed outlier: 3.755A pdb=" N ILE G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU G 136 " --> pdb=" O ARG G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 176 removed outlier: 3.879A pdb=" N ASP G 166 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN G 176 " --> pdb=" O LEU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 188 removed outlier: 3.553A pdb=" N LYS G 182 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'G' and resid 195 through 206 removed outlier: 4.144A pdb=" N ILE G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 217 Processing helix chain 'H' and resid 16 through 30 Processing helix chain 'H' and resid 35 through 44 Processing helix chain 'H' and resid 48 through 58 removed outlier: 3.739A pdb=" N THR H 58 " --> pdb=" O THR H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 84 Processing helix chain 'H' and resid 100 through 105 removed outlier: 3.670A pdb=" N ALA H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 125 through 146 removed outlier: 3.608A pdb=" N LYS H 140 " --> pdb=" O LEU H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 153 removed outlier: 3.590A pdb=" N ILE H 153 " --> pdb=" O ILE H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 175 Processing helix chain 'H' and resid 178 through 193 removed outlier: 4.606A pdb=" N LEU H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 removed outlier: 3.683A pdb=" N THR H 200 " --> pdb=" O PRO H 196 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE H 201 " --> pdb=" O ASP H 197 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY H 206 " --> pdb=" O LEU H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 218 removed outlier: 3.569A pdb=" N CYS H 218 " --> pdb=" O MET H 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 30 Processing helix chain 'I' and resid 35 through 43 Processing helix chain 'I' and resid 48 through 58 Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 110 through 120 Processing helix chain 'I' and resid 125 through 145 Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 160 through 175 Processing helix chain 'J' and resid 178 through 193 removed outlier: 4.424A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 206 removed outlier: 3.539A pdb=" N THR J 200 " --> pdb=" O PRO J 196 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'P' and resid 16 through 31 removed outlier: 3.724A pdb=" N LEU P 20 " --> pdb=" O SER P 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN P 21 " --> pdb=" O PRO P 17 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU P 29 " --> pdb=" O LYS P 25 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA P 31 " --> pdb=" O VAL P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 35 through 44 removed outlier: 3.726A pdb=" N MET P 39 " --> pdb=" O GLU P 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER P 44 " --> pdb=" O PHE P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 57 removed outlier: 3.567A pdb=" N ASN P 53 " --> pdb=" O PRO P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 61 removed outlier: 3.981A pdb=" N GLY P 61 " --> pdb=" O THR P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 61' Processing helix chain 'P' and resid 62 through 81 removed outlier: 3.551A pdb=" N MET P 68 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU P 69 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 105 Processing helix chain 'P' and resid 110 through 119 Processing helix chain 'P' and resid 125 through 146 removed outlier: 3.755A pdb=" N ILE P 129 " --> pdb=" O PRO P 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU P 136 " --> pdb=" O ARG P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 153 Processing helix chain 'P' and resid 160 through 176 removed outlier: 3.881A pdb=" N ASP P 166 " --> pdb=" O ARG P 162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN P 176 " --> pdb=" O LEU P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 188 removed outlier: 3.553A pdb=" N LYS P 182 " --> pdb=" O SER P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 193 Processing helix chain 'P' and resid 195 through 206 removed outlier: 4.144A pdb=" N ILE P 201 " --> pdb=" O ASP P 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY P 206 " --> pdb=" O LEU P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 217 Processing helix chain 'Q' and resid 16 through 30 Processing helix chain 'Q' and resid 35 through 44 Processing helix chain 'Q' and resid 48 through 58 removed outlier: 3.739A pdb=" N THR Q 58 " --> pdb=" O THR Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 84 Processing helix chain 'Q' and resid 100 through 105 removed outlier: 3.670A pdb=" N ALA Q 105 " --> pdb=" O GLY Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 120 Processing helix chain 'Q' and resid 125 through 146 removed outlier: 3.608A pdb=" N LYS Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 153 removed outlier: 3.590A pdb=" N ILE Q 153 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 175 Processing helix chain 'Q' and resid 178 through 193 removed outlier: 4.606A pdb=" N LEU Q 190 " --> pdb=" O THR Q 186 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL Q 191 " --> pdb=" O GLU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 206 removed outlier: 3.683A pdb=" N THR Q 200 " --> pdb=" O PRO Q 196 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE Q 201 " --> pdb=" O ASP Q 197 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY Q 206 " --> pdb=" O LEU Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 218 removed outlier: 3.569A pdb=" N CYS Q 218 " --> pdb=" O MET Q 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 30 Processing helix chain 'R' and resid 35 through 43 Processing helix chain 'R' and resid 48 through 58 Processing helix chain 'R' and resid 62 through 84 Processing helix chain 'R' and resid 110 through 120 Processing helix chain 'R' and resid 125 through 145 Processing helix chain 'S' and resid 149 through 153 Processing helix chain 'S' and resid 160 through 175 Processing helix chain 'S' and resid 178 through 193 removed outlier: 4.424A pdb=" N LEU S 190 " --> pdb=" O THR S 186 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL S 191 " --> pdb=" O GLU S 187 " (cutoff:3.500A) Processing helix chain 'S' and resid 195 through 206 removed outlier: 3.539A pdb=" N THR S 200 " --> pdb=" O PRO S 196 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE S 201 " --> pdb=" O ASP S 197 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY S 206 " --> pdb=" O LEU S 202 " (cutoff:3.500A) Processing helix chain 'S' and resid 210 through 218 Processing helix chain 'V' and resid 16 through 31 removed outlier: 3.725A pdb=" N LEU V 20 " --> pdb=" O SER V 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN V 21 " --> pdb=" O PRO V 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU V 29 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA V 31 " --> pdb=" O VAL V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 44 removed outlier: 3.726A pdb=" N MET V 39 " --> pdb=" O GLU V 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER V 44 " --> pdb=" O PHE V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 57 removed outlier: 3.567A pdb=" N ASN V 53 " --> pdb=" O PRO V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 61 removed outlier: 3.980A pdb=" N GLY V 61 " --> pdb=" O THR V 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 58 through 61' Processing helix chain 'V' and resid 62 through 81 removed outlier: 3.551A pdb=" N MET V 68 " --> pdb=" O ALA V 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU V 69 " --> pdb=" O ALA V 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP V 81 " --> pdb=" O ALA V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 105 Processing helix chain 'V' and resid 110 through 119 Processing helix chain 'V' and resid 125 through 146 removed outlier: 3.755A pdb=" N ILE V 129 " --> pdb=" O PRO V 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU V 136 " --> pdb=" O ARG V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 153 Processing helix chain 'V' and resid 160 through 176 removed outlier: 3.880A pdb=" N ASP V 166 " --> pdb=" O ARG V 162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN V 176 " --> pdb=" O LEU V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 188 removed outlier: 3.553A pdb=" N LYS V 182 " --> pdb=" O SER V 178 " (cutoff:3.500A) Processing helix chain 'V' and resid 188 through 193 Processing helix chain 'V' and resid 195 through 206 removed outlier: 4.144A pdb=" N ILE V 201 " --> pdb=" O ASP V 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY V 206 " --> pdb=" O LEU V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 210 through 217 Processing helix chain 'W' and resid 16 through 30 Processing helix chain 'W' and resid 35 through 44 Processing helix chain 'W' and resid 48 through 58 removed outlier: 3.740A pdb=" N THR W 58 " --> pdb=" O THR W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 84 Processing helix chain 'W' and resid 100 through 105 removed outlier: 3.670A pdb=" N ALA W 105 " --> pdb=" O GLY W 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 120 Processing helix chain 'W' and resid 125 through 146 removed outlier: 3.607A pdb=" N LYS W 140 " --> pdb=" O LEU W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 149 through 153 removed outlier: 3.590A pdb=" N ILE W 153 " --> pdb=" O ILE W 150 " (cutoff:3.500A) Processing helix chain 'W' and resid 160 through 175 Processing helix chain 'W' and resid 178 through 193 removed outlier: 4.605A pdb=" N LEU W 190 " --> pdb=" O THR W 186 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL W 191 " --> pdb=" O GLU W 187 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 206 removed outlier: 3.683A pdb=" N THR W 200 " --> pdb=" O PRO W 196 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE W 201 " --> pdb=" O ASP W 197 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY W 206 " --> pdb=" O LEU W 202 " (cutoff:3.500A) Processing helix chain 'W' and resid 210 through 218 removed outlier: 3.569A pdb=" N CYS W 218 " --> pdb=" O MET W 214 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 30 Processing helix chain 'X' and resid 35 through 43 Processing helix chain 'X' and resid 48 through 58 Processing helix chain 'X' and resid 62 through 84 Processing helix chain 'X' and resid 110 through 120 Processing helix chain 'X' and resid 125 through 145 Processing helix chain '0' and resid 149 through 153 Processing helix chain '0' and resid 160 through 175 Processing helix chain '0' and resid 178 through 193 removed outlier: 4.423A pdb=" N LEU 0 190 " --> pdb=" O THR 0 186 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL 0 191 " --> pdb=" O GLU 0 187 " (cutoff:3.500A) Processing helix chain '0' and resid 195 through 206 removed outlier: 3.539A pdb=" N THR 0 200 " --> pdb=" O PRO 0 196 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE 0 201 " --> pdb=" O ASP 0 197 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY 0 206 " --> pdb=" O LEU 0 202 " (cutoff:3.500A) Processing helix chain '0' and resid 210 through 218 Processing helix chain '3' and resid 16 through 31 removed outlier: 3.724A pdb=" N LEU 3 20 " --> pdb=" O SER 3 16 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN 3 21 " --> pdb=" O PRO 3 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU 3 29 " --> pdb=" O LYS 3 25 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA 3 31 " --> pdb=" O VAL 3 27 " (cutoff:3.500A) Processing helix chain '3' and resid 35 through 44 removed outlier: 3.726A pdb=" N MET 3 39 " --> pdb=" O GLU 3 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER 3 44 " --> pdb=" O PHE 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 48 through 57 removed outlier: 3.567A pdb=" N ASN 3 53 " --> pdb=" O PRO 3 49 " (cutoff:3.500A) Processing helix chain '3' and resid 58 through 61 removed outlier: 3.981A pdb=" N GLY 3 61 " --> pdb=" O THR 3 58 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 58 through 61' Processing helix chain '3' and resid 62 through 81 removed outlier: 3.551A pdb=" N MET 3 68 " --> pdb=" O ALA 3 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 3 69 " --> pdb=" O ALA 3 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP 3 81 " --> pdb=" O ALA 3 77 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 105 Processing helix chain '3' and resid 110 through 119 Processing helix chain '3' and resid 125 through 146 removed outlier: 3.755A pdb=" N ILE 3 129 " --> pdb=" O PRO 3 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU 3 136 " --> pdb=" O ARG 3 132 " (cutoff:3.500A) Processing helix chain '3' and resid 149 through 153 Processing helix chain '3' and resid 160 through 176 removed outlier: 3.880A pdb=" N ASP 3 166 " --> pdb=" O ARG 3 162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN 3 176 " --> pdb=" O LEU 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 178 through 188 removed outlier: 3.553A pdb=" N LYS 3 182 " --> pdb=" O SER 3 178 " (cutoff:3.500A) Processing helix chain '3' and resid 188 through 193 Processing helix chain '3' and resid 195 through 206 removed outlier: 4.144A pdb=" N ILE 3 201 " --> pdb=" O ASP 3 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY 3 206 " --> pdb=" O LEU 3 202 " (cutoff:3.500A) Processing helix chain '3' and resid 210 through 217 1420 hydrogen bonds defined for protein. 4185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7190 1.34 - 1.46: 3993 1.46 - 1.57: 11232 1.57 - 1.69: 0 1.69 - 1.81: 275 Bond restraints: 22690 Sorted by residual: bond pdb=" C SER V 146 " pdb=" N PRO V 147 " ideal model delta sigma weight residual 1.336 1.319 0.017 1.20e-02 6.94e+03 1.91e+00 bond pdb=" C SER G 146 " pdb=" N PRO G 147 " ideal model delta sigma weight residual 1.336 1.320 0.016 1.20e-02 6.94e+03 1.89e+00 bond pdb=" C SER 3 146 " pdb=" N PRO 3 147 " ideal model delta sigma weight residual 1.336 1.320 0.016 1.20e-02 6.94e+03 1.88e+00 bond pdb=" C SER A 146 " pdb=" N PRO A 147 " ideal model delta sigma weight residual 1.336 1.320 0.016 1.20e-02 6.94e+03 1.86e+00 bond pdb=" C SER P 146 " pdb=" N PRO P 147 " ideal model delta sigma weight residual 1.336 1.320 0.016 1.20e-02 6.94e+03 1.76e+00 ... (remaining 22685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 30203 1.26 - 2.53: 651 2.53 - 3.79: 253 3.79 - 5.06: 18 5.06 - 6.32: 15 Bond angle restraints: 31140 Sorted by residual: angle pdb=" C LEU F 315 " pdb=" N PHE F 316 " pdb=" CA PHE F 316 " ideal model delta sigma weight residual 121.48 115.16 6.32 2.04e+00 2.40e-01 9.60e+00 angle pdb=" C LEU Z 315 " pdb=" N PHE Z 316 " pdb=" CA PHE Z 316 " ideal model delta sigma weight residual 121.48 115.17 6.31 2.04e+00 2.40e-01 9.55e+00 angle pdb=" C LEU U 315 " pdb=" N PHE U 316 " pdb=" CA PHE U 316 " ideal model delta sigma weight residual 121.48 115.18 6.30 2.04e+00 2.40e-01 9.54e+00 angle pdb=" C LEU O 315 " pdb=" N PHE O 316 " pdb=" CA PHE O 316 " ideal model delta sigma weight residual 121.48 115.19 6.29 2.04e+00 2.40e-01 9.51e+00 angle pdb=" C LEU 2 315 " pdb=" N PHE 2 316 " pdb=" CA PHE 2 316 " ideal model delta sigma weight residual 121.48 115.23 6.25 2.04e+00 2.40e-01 9.39e+00 ... (remaining 31135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 12435 14.77 - 29.54: 775 29.54 - 44.31: 195 44.31 - 59.08: 75 59.08 - 73.85: 5 Dihedral angle restraints: 13485 sinusoidal: 4600 harmonic: 8885 Sorted by residual: dihedral pdb=" N ARG G 18 " pdb=" CA ARG G 18 " pdb=" CB ARG G 18 " pdb=" CG ARG G 18 " ideal model delta sinusoidal sigma weight residual -60.00 -117.97 57.97 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N ARG 3 18 " pdb=" CA ARG 3 18 " pdb=" CB ARG 3 18 " pdb=" CG ARG 3 18 " ideal model delta sinusoidal sigma weight residual -60.00 -117.96 57.96 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N ARG P 18 " pdb=" CA ARG P 18 " pdb=" CB ARG P 18 " pdb=" CG ARG P 18 " ideal model delta sinusoidal sigma weight residual -60.00 -117.95 57.95 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 13482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2175 0.028 - 0.055: 1006 0.055 - 0.083: 362 0.083 - 0.111: 148 0.111 - 0.138: 39 Chirality restraints: 3730 Sorted by residual: chirality pdb=" CA PRO H 34 " pdb=" N PRO H 34 " pdb=" C PRO H 34 " pdb=" CB PRO H 34 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA PRO B 34 " pdb=" N PRO B 34 " pdb=" C PRO B 34 " pdb=" CB PRO B 34 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA PRO W 34 " pdb=" N PRO W 34 " pdb=" C PRO W 34 " pdb=" CB PRO W 34 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 3727 not shown) Planarity restraints: 3980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 33 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 34 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 34 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 34 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER W 33 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.64e+00 pdb=" N PRO W 34 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO W 34 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO W 34 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 33 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO L 34 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 34 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 34 " 0.023 5.00e-02 4.00e+02 ... (remaining 3977 not shown) Histogram of nonbonded interaction distances: 0.64 - 1.49: 15 1.49 - 2.34: 95 2.34 - 3.19: 22118 3.19 - 4.05: 53403 4.05 - 4.90: 91999 Warning: very small nonbonded interaction distances. Nonbonded interactions: 167630 Sorted by model distance: nonbonded pdb=" CB GLU A 35 " pdb=" OE2 GLU G 28 " model vdw 0.636 3.440 nonbonded pdb=" CB GLU V 35 " pdb=" OE2 GLU 3 28 " model vdw 0.636 3.440 nonbonded pdb=" CB GLU G 35 " pdb=" OE2 GLU P 28 " model vdw 0.636 3.440 nonbonded pdb=" OE2 GLU A 28 " pdb=" CB GLU 3 35 " model vdw 0.636 3.440 nonbonded pdb=" CB GLU P 35 " pdb=" OE2 GLU V 28 " model vdw 0.636 3.440 ... (remaining 167625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'B' selection = chain 'H' selection = chain 'Q' selection = chain 'W' } ncs_group { reference = chain 'M' selection = chain 'C' selection = chain 'I' selection = chain 'R' selection = chain 'X' } ncs_group { reference = chain 'N' selection = chain 'D' selection = chain 'J' selection = chain 'S' selection = chain '0' } ncs_group { reference = chain 'Y' selection = chain 'E' selection = chain 'K' selection = chain 'T' selection = chain '1' } ncs_group { reference = chain 'Z' selection = chain 'F' selection = chain 'O' selection = chain 'U' selection = chain '2' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'P' selection = chain 'V' selection = chain '3' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.100 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.005 0.029 22690 Z= 0.226 Angle : 0.545 6.319 31140 Z= 0.287 Chirality : 0.039 0.138 3730 Planarity : 0.004 0.041 3980 Dihedral : 11.630 73.846 7695 Min Nonbonded Distance : 0.636 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.04 % Allowed : 7.26 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.16), residues: 2985 helix: 1.34 (0.12), residues: 1990 sheet: None (None), residues: 0 loop : 1.06 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 18 TYR 0.008 0.001 TYR G 145 PHE 0.008 0.002 PHE W 168 TRP 0.009 0.001 TRP D 184 HIS 0.002 0.001 HIS I 120 Details of bonding type rmsd covalent geometry : bond 0.00510 (22690) covalent geometry : angle 0.54490 (31140) hydrogen bonds : bond 0.20883 ( 1420) hydrogen bonds : angle 6.73311 ( 4185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 531 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8955 (m-30) cc_final: 0.8573 (m-30) REVERT: L 144 MET cc_start: 0.8709 (ttm) cc_final: 0.8444 (ttm) REVERT: L 214 MET cc_start: 0.9256 (mtm) cc_final: 0.9012 (mtp) REVERT: M 35 GLU cc_start: 0.8665 (pt0) cc_final: 0.8362 (tt0) REVERT: M 39 MET cc_start: 0.9085 (tpp) cc_final: 0.8807 (tpt) REVERT: N 164 TYR cc_start: 0.8991 (t80) cc_final: 0.8281 (t80) REVERT: N 192 GLN cc_start: 0.8946 (tp40) cc_final: 0.8612 (tp-100) REVERT: N 214 MET cc_start: 0.9114 (mtp) cc_final: 0.8800 (mtt) REVERT: Z 316 PHE cc_start: 0.8411 (m-80) cc_final: 0.7542 (m-80) REVERT: A 51 ASP cc_start: 0.9007 (m-30) cc_final: 0.8781 (m-30) REVERT: A 59 VAL cc_start: 0.9492 (OUTLIER) cc_final: 0.9236 (p) REVERT: B 67 GLN cc_start: 0.8808 (tp40) cc_final: 0.8300 (tp40) REVERT: B 84 HIS cc_start: 0.8443 (m90) cc_final: 0.8084 (m90) REVERT: B 214 MET cc_start: 0.9256 (mtm) cc_final: 0.9034 (mtp) REVERT: C 32 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: C 35 GLU cc_start: 0.8760 (pt0) cc_final: 0.8445 (tt0) REVERT: C 39 MET cc_start: 0.9226 (tpp) cc_final: 0.8947 (tpt) REVERT: D 164 TYR cc_start: 0.8925 (t80) cc_final: 0.8164 (t80) REVERT: D 171 THR cc_start: 0.9396 (m) cc_final: 0.9113 (p) REVERT: G 185 MET cc_start: 0.9204 (mtt) cc_final: 0.8985 (mtm) REVERT: H 26 VAL cc_start: 0.9431 (t) cc_final: 0.9219 (t) REVERT: H 67 GLN cc_start: 0.8957 (tp40) cc_final: 0.8700 (tp40) REVERT: H 84 HIS cc_start: 0.8339 (m90) cc_final: 0.8026 (m90) REVERT: I 35 GLU cc_start: 0.8621 (pt0) cc_final: 0.8298 (tt0) REVERT: J 164 TYR cc_start: 0.8973 (t80) cc_final: 0.8501 (t80) REVERT: J 214 MET cc_start: 0.9113 (mtp) cc_final: 0.8841 (mtt) REVERT: P 51 ASP cc_start: 0.8920 (m-30) cc_final: 0.8649 (m-30) REVERT: Q 51 ASP cc_start: 0.8855 (m-30) cc_final: 0.8471 (m-30) REVERT: Q 67 GLN cc_start: 0.8812 (tp40) cc_final: 0.8528 (tp40) REVERT: Q 84 HIS cc_start: 0.8504 (m90) cc_final: 0.8061 (m90) REVERT: Q 214 MET cc_start: 0.9302 (mtm) cc_final: 0.9096 (mtp) REVERT: R 35 GLU cc_start: 0.8699 (pt0) cc_final: 0.8092 (tp30) REVERT: R 39 MET cc_start: 0.9269 (tpp) cc_final: 0.9060 (tpt) REVERT: S 164 TYR cc_start: 0.8974 (t80) cc_final: 0.8237 (t80) REVERT: S 214 MET cc_start: 0.9097 (mtp) cc_final: 0.8797 (mtt) REVERT: S 215 MET cc_start: 0.9065 (mtm) cc_final: 0.8814 (mtm) REVERT: V 144 MET cc_start: 0.9051 (ttm) cc_final: 0.8784 (ttm) REVERT: W 67 GLN cc_start: 0.8824 (tp40) cc_final: 0.8460 (tp40) REVERT: W 114 GLN cc_start: 0.9284 (mt0) cc_final: 0.9070 (mt0) REVERT: X 35 GLU cc_start: 0.8512 (pt0) cc_final: 0.8066 (tt0) REVERT: 0 164 TYR cc_start: 0.9010 (t80) cc_final: 0.8386 (t80) REVERT: 3 51 ASP cc_start: 0.8946 (m-30) cc_final: 0.8728 (m-30) outliers start: 65 outliers final: 36 residues processed: 581 average time/residue: 0.1402 time to fit residues: 131.6644 Evaluate side-chains 427 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 389 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 144 MET Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 32 PHE Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain R residue 32 PHE Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 144 MET Chi-restraints excluded: chain 0 residue 150 ILE Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 3 residue 33 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.0270 chunk 207 optimal weight: 0.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 overall best weight: 1.8048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 155 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 ASN N 179 GLN A 112 GLN A 195 ASN B 155 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN D 179 GLN G 112 GLN G 195 ASN H 155 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN J 179 GLN ** O 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 195 ASN Q 155 GLN ** Q 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 193 ASN S 179 GLN V 195 ASN W 155 GLN ** W 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 193 ASN 0 179 GLN 3 195 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.075687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056554 restraints weight = 82442.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.058276 restraints weight = 49243.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.059375 restraints weight = 35932.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.060096 restraints weight = 29706.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.060557 restraints weight = 26401.972| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22690 Z= 0.141 Angle : 0.563 8.057 31140 Z= 0.289 Chirality : 0.041 0.170 3730 Planarity : 0.005 0.049 3980 Dihedral : 6.029 57.456 3213 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.12 % Allowed : 13.30 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.15), residues: 2985 helix: 1.73 (0.11), residues: 2125 sheet: None (None), residues: 0 loop : 0.90 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 82 TYR 0.020 0.002 TYR B 164 PHE 0.015 0.001 PHE G 161 TRP 0.012 0.001 TRP C 133 HIS 0.004 0.001 HIS M 62 Details of bonding type rmsd covalent geometry : bond 0.00316 (22690) covalent geometry : angle 0.56287 (31140) hydrogen bonds : bond 0.04851 ( 1420) hydrogen bonds : angle 4.43251 ( 4185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 523 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8963 (m-30) cc_final: 0.8397 (m-30) REVERT: L 55 MET cc_start: 0.9201 (ttp) cc_final: 0.8929 (tmm) REVERT: L 117 TRP cc_start: 0.8561 (OUTLIER) cc_final: 0.8191 (m-90) REVERT: L 143 ARG cc_start: 0.9187 (tpt90) cc_final: 0.8507 (tpm170) REVERT: L 144 MET cc_start: 0.8803 (ttm) cc_final: 0.8287 (ttm) REVERT: L 214 MET cc_start: 0.9065 (mtm) cc_final: 0.8761 (mtp) REVERT: M 35 GLU cc_start: 0.8757 (pt0) cc_final: 0.8323 (tt0) REVERT: M 76 GLU cc_start: 0.8628 (tp30) cc_final: 0.8397 (tp30) REVERT: M 114 GLN cc_start: 0.9234 (mt0) cc_final: 0.8511 (mp10) REVERT: N 164 TYR cc_start: 0.8968 (t80) cc_final: 0.8340 (t80) REVERT: N 192 GLN cc_start: 0.8915 (tp40) cc_final: 0.8549 (tp-100) REVERT: A 45 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8457 (tm-30) REVERT: A 51 ASP cc_start: 0.9205 (m-30) cc_final: 0.9002 (m-30) REVERT: B 67 GLN cc_start: 0.8698 (tp40) cc_final: 0.8381 (tp40) REVERT: B 117 TRP cc_start: 0.8398 (OUTLIER) cc_final: 0.8024 (m-90) REVERT: C 32 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: C 35 GLU cc_start: 0.8788 (pt0) cc_final: 0.8111 (tt0) REVERT: C 39 MET cc_start: 0.9205 (tpp) cc_final: 0.8976 (mmm) REVERT: C 76 GLU cc_start: 0.8689 (tp30) cc_final: 0.8350 (tp30) REVERT: C 82 ARG cc_start: 0.8313 (tmm160) cc_final: 0.7977 (ttp80) REVERT: C 114 GLN cc_start: 0.9159 (mt0) cc_final: 0.8415 (mp-120) REVERT: D 164 TYR cc_start: 0.8910 (t80) cc_final: 0.8040 (t80) REVERT: D 171 THR cc_start: 0.9289 (m) cc_final: 0.8957 (p) REVERT: D 192 GLN cc_start: 0.8929 (tp40) cc_final: 0.8688 (tp-100) REVERT: G 29 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8035 (mt-10) REVERT: G 55 MET cc_start: 0.9067 (mtp) cc_final: 0.8720 (mtp) REVERT: G 109 SER cc_start: 0.7111 (OUTLIER) cc_final: 0.6861 (m) REVERT: G 185 MET cc_start: 0.9191 (mtt) cc_final: 0.8976 (mtm) REVERT: G 215 MET cc_start: 0.8883 (mtt) cc_final: 0.8575 (mmt) REVERT: H 51 ASP cc_start: 0.9096 (m-30) cc_final: 0.8388 (m-30) REVERT: H 55 MET cc_start: 0.9227 (ttp) cc_final: 0.9008 (tmm) REVERT: H 67 GLN cc_start: 0.8708 (tp40) cc_final: 0.8447 (tp40) REVERT: H 84 HIS cc_start: 0.8276 (m90) cc_final: 0.7988 (m90) REVERT: I 35 GLU cc_start: 0.8515 (pt0) cc_final: 0.8158 (tp30) REVERT: I 114 GLN cc_start: 0.9265 (mt0) cc_final: 0.8582 (mp10) REVERT: J 164 TYR cc_start: 0.8891 (t80) cc_final: 0.8509 (t80) REVERT: P 66 MET cc_start: 0.9037 (tpt) cc_final: 0.8791 (tpt) REVERT: P 109 SER cc_start: 0.7129 (OUTLIER) cc_final: 0.6821 (m) REVERT: P 195 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8912 (p0) REVERT: P 215 MET cc_start: 0.8759 (mtt) cc_final: 0.8480 (mtt) REVERT: Q 51 ASP cc_start: 0.8882 (m-30) cc_final: 0.8356 (m-30) REVERT: Q 117 TRP cc_start: 0.8608 (OUTLIER) cc_final: 0.8363 (m-90) REVERT: Q 179 GLN cc_start: 0.7843 (tp40) cc_final: 0.7093 (tp40) REVERT: R 35 GLU cc_start: 0.8967 (pt0) cc_final: 0.8068 (tp30) REVERT: R 76 GLU cc_start: 0.8717 (tp30) cc_final: 0.8399 (tp30) REVERT: R 114 GLN cc_start: 0.9330 (mt0) cc_final: 0.8667 (mp-120) REVERT: S 164 TYR cc_start: 0.8966 (t80) cc_final: 0.8219 (t80) REVERT: V 109 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.7049 (m) REVERT: V 215 MET cc_start: 0.8760 (mtt) cc_final: 0.8288 (mtt) REVERT: W 51 ASP cc_start: 0.8978 (m-30) cc_final: 0.8455 (m-30) REVERT: W 53 ASN cc_start: 0.8874 (m-40) cc_final: 0.8420 (t0) REVERT: W 67 GLN cc_start: 0.8684 (tp40) cc_final: 0.8327 (tp40) REVERT: X 35 GLU cc_start: 0.8773 (pt0) cc_final: 0.8033 (tt0) REVERT: X 114 GLN cc_start: 0.9233 (mt0) cc_final: 0.8521 (mp10) REVERT: 0 164 TYR cc_start: 0.8957 (t80) cc_final: 0.8431 (t80) REVERT: 3 51 ASP cc_start: 0.9197 (m-30) cc_final: 0.8936 (m-30) REVERT: 3 66 MET cc_start: 0.8870 (tpt) cc_final: 0.8336 (tpp) REVERT: 3 109 SER cc_start: 0.7396 (OUTLIER) cc_final: 0.7195 (m) REVERT: 3 128 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7716 (tm-30) REVERT: 3 195 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8822 (p0) REVERT: 3 215 MET cc_start: 0.8875 (mtt) cc_final: 0.8675 (mtt) outliers start: 88 outliers final: 48 residues processed: 576 average time/residue: 0.1350 time to fit residues: 124.9365 Evaluate side-chains 465 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 407 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 117 TRP Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 144 MET Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 109 SER Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 117 TRP Chi-restraints excluded: chain R residue 32 PHE Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 195 ASN Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 150 ILE Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 202 LEU Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 144 MET Chi-restraints excluded: chain 3 residue 150 ILE Chi-restraints excluded: chain 3 residue 195 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 21 optimal weight: 7.9990 chunk 128 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 243 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 GLN P 195 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN V 112 GLN 2 319 GLN 3 195 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.074237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.055052 restraints weight = 84345.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.056589 restraints weight = 52845.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057580 restraints weight = 39826.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.058201 restraints weight = 33524.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.058481 restraints weight = 30241.767| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22690 Z= 0.194 Angle : 0.596 8.969 31140 Z= 0.304 Chirality : 0.041 0.169 3730 Planarity : 0.005 0.055 3980 Dihedral : 5.353 55.783 3192 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.84 % Allowed : 15.83 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.15), residues: 2985 helix: 1.61 (0.11), residues: 2095 sheet: None (None), residues: 0 loop : 1.09 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 82 TYR 0.021 0.001 TYR L 164 PHE 0.011 0.001 PHE V 40 TRP 0.032 0.001 TRP H 117 HIS 0.004 0.001 HIS M 84 Details of bonding type rmsd covalent geometry : bond 0.00455 (22690) covalent geometry : angle 0.59650 (31140) hydrogen bonds : bond 0.04684 ( 1420) hydrogen bonds : angle 4.45070 ( 4185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 428 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8921 (m-30) cc_final: 0.8340 (m-30) REVERT: L 144 MET cc_start: 0.8780 (ttm) cc_final: 0.8394 (ttm) REVERT: L 214 MET cc_start: 0.9102 (mtm) cc_final: 0.8850 (mtp) REVERT: M 35 GLU cc_start: 0.8780 (pt0) cc_final: 0.8282 (tt0) REVERT: M 76 GLU cc_start: 0.8635 (tp30) cc_final: 0.8369 (tp30) REVERT: M 114 GLN cc_start: 0.9301 (mt0) cc_final: 0.8659 (mp10) REVERT: N 164 TYR cc_start: 0.8990 (t80) cc_final: 0.8365 (t80) REVERT: N 192 GLN cc_start: 0.8923 (tp40) cc_final: 0.8582 (tp-100) REVERT: N 215 MET cc_start: 0.8916 (ttp) cc_final: 0.8617 (ttp) REVERT: A 51 ASP cc_start: 0.9152 (m-30) cc_final: 0.8934 (m-30) REVERT: B 51 ASP cc_start: 0.8936 (m-30) cc_final: 0.8282 (m-30) REVERT: C 32 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7553 (m-80) REVERT: C 35 GLU cc_start: 0.8912 (pt0) cc_final: 0.8200 (tt0) REVERT: C 39 MET cc_start: 0.9165 (tpp) cc_final: 0.8585 (mmm) REVERT: C 76 GLU cc_start: 0.8732 (tp30) cc_final: 0.8349 (tp30) REVERT: C 114 GLN cc_start: 0.9205 (mt0) cc_final: 0.8502 (mp10) REVERT: D 164 TYR cc_start: 0.8891 (t80) cc_final: 0.8087 (t80) REVERT: D 171 THR cc_start: 0.9330 (m) cc_final: 0.9014 (p) REVERT: D 192 GLN cc_start: 0.8944 (tp40) cc_final: 0.8684 (tp-100) REVERT: G 55 MET cc_start: 0.9127 (mtp) cc_final: 0.8790 (mtp) REVERT: H 51 ASP cc_start: 0.9042 (m-30) cc_final: 0.8389 (m-30) REVERT: H 67 GLN cc_start: 0.8799 (tp40) cc_final: 0.8527 (tp40) REVERT: I 82 ARG cc_start: 0.8311 (tmm160) cc_final: 0.8016 (ttp80) REVERT: I 114 GLN cc_start: 0.9356 (mt0) cc_final: 0.8773 (mp10) REVERT: J 164 TYR cc_start: 0.8915 (t80) cc_final: 0.8571 (t80) REVERT: P 44 SER cc_start: 0.8877 (m) cc_final: 0.8668 (p) REVERT: P 66 MET cc_start: 0.9037 (tpt) cc_final: 0.8783 (tpt) REVERT: P 215 MET cc_start: 0.8627 (mtt) cc_final: 0.8403 (mtt) REVERT: Q 51 ASP cc_start: 0.8914 (m-30) cc_final: 0.8402 (m-30) REVERT: Q 179 GLN cc_start: 0.7816 (tp40) cc_final: 0.7091 (tp40) REVERT: R 35 GLU cc_start: 0.8794 (pt0) cc_final: 0.8010 (tt0) REVERT: R 76 GLU cc_start: 0.8771 (tp30) cc_final: 0.8432 (tp30) REVERT: R 114 GLN cc_start: 0.9290 (mt0) cc_final: 0.8696 (mp10) REVERT: S 164 TYR cc_start: 0.8986 (t80) cc_final: 0.8375 (t80) REVERT: V 215 MET cc_start: 0.8652 (mtt) cc_final: 0.8331 (mtt) REVERT: W 51 ASP cc_start: 0.8978 (m-30) cc_final: 0.8453 (m-30) REVERT: W 53 ASN cc_start: 0.8871 (m-40) cc_final: 0.8366 (t0) REVERT: W 67 GLN cc_start: 0.8684 (tp40) cc_final: 0.8412 (tp40) REVERT: X 35 GLU cc_start: 0.8729 (pt0) cc_final: 0.8033 (tt0) REVERT: X 114 GLN cc_start: 0.9342 (mt0) cc_final: 0.8722 (mp10) REVERT: 0 164 TYR cc_start: 0.8947 (t80) cc_final: 0.8459 (t80) REVERT: 3 51 ASP cc_start: 0.9100 (m-30) cc_final: 0.8861 (m-30) REVERT: 3 66 MET cc_start: 0.8901 (tpt) cc_final: 0.8381 (tpp) REVERT: 3 185 MET cc_start: 0.9219 (mtm) cc_final: 0.8984 (mtm) outliers start: 82 outliers final: 52 residues processed: 487 average time/residue: 0.1444 time to fit residues: 111.9421 Evaluate side-chains 448 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 395 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 144 MET Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 150 ILE Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 144 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 82 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 299 optimal weight: 0.8980 chunk 217 optimal weight: 40.0000 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 ASN A 112 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 GLN P 112 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 219 GLN V 112 GLN W 179 GLN 0 195 ASN 0 219 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.054689 restraints weight = 84863.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.056252 restraints weight = 52615.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057256 restraints weight = 39436.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.057875 restraints weight = 33165.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.058270 restraints weight = 29912.294| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22690 Z= 0.204 Angle : 0.592 9.043 31140 Z= 0.302 Chirality : 0.041 0.169 3730 Planarity : 0.005 0.057 3980 Dihedral : 5.206 55.442 3187 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.37 % Allowed : 17.56 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.15), residues: 2985 helix: 1.52 (0.11), residues: 2130 sheet: None (None), residues: 0 loop : 1.07 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 82 TYR 0.024 0.002 TYR L 164 PHE 0.012 0.001 PHE 3 40 TRP 0.017 0.001 TRP H 117 HIS 0.004 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00479 (22690) covalent geometry : angle 0.59155 (31140) hydrogen bonds : bond 0.04477 ( 1420) hydrogen bonds : angle 4.43572 ( 4185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 423 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8910 (m-30) cc_final: 0.8311 (m-30) REVERT: L 144 MET cc_start: 0.8766 (ttm) cc_final: 0.8168 (ttm) REVERT: M 35 GLU cc_start: 0.8764 (pt0) cc_final: 0.8286 (tt0) REVERT: M 76 GLU cc_start: 0.8695 (tp30) cc_final: 0.8417 (tp30) REVERT: M 114 GLN cc_start: 0.9362 (mt0) cc_final: 0.8864 (mp10) REVERT: N 164 TYR cc_start: 0.8989 (t80) cc_final: 0.8304 (t80) REVERT: N 192 GLN cc_start: 0.8927 (tp40) cc_final: 0.8570 (tp-100) REVERT: N 215 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8601 (ttp) REVERT: A 51 ASP cc_start: 0.9155 (m-30) cc_final: 0.8908 (m-30) REVERT: B 51 ASP cc_start: 0.8916 (m-30) cc_final: 0.8284 (m-30) REVERT: C 32 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: C 35 GLU cc_start: 0.8898 (pt0) cc_final: 0.8066 (tt0) REVERT: C 76 GLU cc_start: 0.8718 (tp30) cc_final: 0.8267 (tp30) REVERT: C 114 GLN cc_start: 0.9233 (mt0) cc_final: 0.8612 (mp10) REVERT: D 164 TYR cc_start: 0.8916 (t80) cc_final: 0.8088 (t80) REVERT: D 171 THR cc_start: 0.9339 (m) cc_final: 0.9013 (p) REVERT: D 192 GLN cc_start: 0.8970 (tp40) cc_final: 0.8665 (tp-100) REVERT: G 55 MET cc_start: 0.9092 (mtp) cc_final: 0.8795 (mtp) REVERT: H 51 ASP cc_start: 0.9010 (m-30) cc_final: 0.8317 (m-30) REVERT: H 67 GLN cc_start: 0.8895 (tp40) cc_final: 0.8578 (tp40) REVERT: H 84 HIS cc_start: 0.8098 (m90) cc_final: 0.7625 (m90) REVERT: I 76 GLU cc_start: 0.8669 (tp30) cc_final: 0.8224 (tp30) REVERT: I 114 GLN cc_start: 0.9361 (mt0) cc_final: 0.8907 (mp10) REVERT: J 164 TYR cc_start: 0.8910 (t80) cc_final: 0.8498 (t80) REVERT: P 44 SER cc_start: 0.8946 (m) cc_final: 0.8729 (p) REVERT: P 66 MET cc_start: 0.9003 (tpt) cc_final: 0.8717 (tpt) REVERT: P 109 SER cc_start: 0.7102 (OUTLIER) cc_final: 0.6724 (m) REVERT: Q 51 ASP cc_start: 0.8926 (m-30) cc_final: 0.8406 (m-30) REVERT: R 35 GLU cc_start: 0.8841 (pt0) cc_final: 0.8076 (tt0) REVERT: R 66 MET cc_start: 0.8868 (mmm) cc_final: 0.8604 (mmm) REVERT: R 76 GLU cc_start: 0.8773 (tp30) cc_final: 0.8363 (tp30) REVERT: R 114 GLN cc_start: 0.9310 (mt0) cc_final: 0.8747 (mp10) REVERT: S 164 TYR cc_start: 0.8960 (t80) cc_final: 0.8391 (t80) REVERT: V 109 SER cc_start: 0.7440 (OUTLIER) cc_final: 0.7101 (m) REVERT: V 215 MET cc_start: 0.8633 (mtt) cc_final: 0.8350 (mtt) REVERT: W 51 ASP cc_start: 0.8955 (m-30) cc_final: 0.8419 (m-30) REVERT: W 55 MET cc_start: 0.9189 (ttt) cc_final: 0.8982 (tmm) REVERT: W 176 GLN cc_start: 0.8326 (mt0) cc_final: 0.8116 (mt0) REVERT: X 35 GLU cc_start: 0.8702 (pt0) cc_final: 0.8084 (tt0) REVERT: X 114 GLN cc_start: 0.9335 (mt0) cc_final: 0.8768 (mp10) REVERT: 0 164 TYR cc_start: 0.8976 (t80) cc_final: 0.8460 (t80) REVERT: 3 51 ASP cc_start: 0.9118 (m-30) cc_final: 0.8906 (m-30) REVERT: 3 66 MET cc_start: 0.8917 (tpt) cc_final: 0.8416 (tpp) outliers start: 72 outliers final: 54 residues processed: 472 average time/residue: 0.1434 time to fit residues: 108.5928 Evaluate side-chains 458 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 400 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 109 SER Chi-restraints excluded: chain R residue 32 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 215 MET Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 150 ILE Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 0 residue 219 GLN Chi-restraints excluded: chain 1 residue 315 LEU Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 35 GLU Chi-restraints excluded: chain 3 residue 71 GLU Chi-restraints excluded: chain 3 residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 155 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 290 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 281 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 GLN W 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.073992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.054661 restraints weight = 83362.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056207 restraints weight = 52074.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.057198 restraints weight = 39217.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057825 restraints weight = 33075.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.058205 restraints weight = 29838.365| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 22690 Z= 0.205 Angle : 0.599 9.626 31140 Z= 0.303 Chirality : 0.041 0.195 3730 Planarity : 0.005 0.057 3980 Dihedral : 5.081 54.286 3181 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.61 % Allowed : 17.89 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.15), residues: 2985 helix: 1.50 (0.11), residues: 2095 sheet: None (None), residues: 0 loop : 1.00 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 82 TYR 0.027 0.001 TYR L 164 PHE 0.013 0.002 PHE 3 40 TRP 0.009 0.001 TRP H 117 HIS 0.004 0.001 HIS R 84 Details of bonding type rmsd covalent geometry : bond 0.00482 (22690) covalent geometry : angle 0.59857 (31140) hydrogen bonds : bond 0.04403 ( 1420) hydrogen bonds : angle 4.41665 ( 4185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 414 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8917 (m-30) cc_final: 0.8292 (m-30) REVERT: L 144 MET cc_start: 0.8687 (ttm) cc_final: 0.8029 (ttm) REVERT: M 35 GLU cc_start: 0.8785 (pt0) cc_final: 0.8289 (tt0) REVERT: M 76 GLU cc_start: 0.8769 (tp30) cc_final: 0.8498 (tp30) REVERT: M 114 GLN cc_start: 0.9369 (mt0) cc_final: 0.8930 (mp10) REVERT: N 164 TYR cc_start: 0.8992 (t80) cc_final: 0.8302 (t80) REVERT: N 192 GLN cc_start: 0.8924 (tp40) cc_final: 0.8568 (tp-100) REVERT: N 215 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8595 (ttp) REVERT: A 51 ASP cc_start: 0.9180 (m-30) cc_final: 0.8929 (m-30) REVERT: A 195 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8635 (p0) REVERT: B 51 ASP cc_start: 0.8903 (m-30) cc_final: 0.8242 (m-30) REVERT: C 32 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: C 35 GLU cc_start: 0.8910 (pt0) cc_final: 0.8032 (tt0) REVERT: C 76 GLU cc_start: 0.8792 (tp30) cc_final: 0.8296 (tp30) REVERT: C 114 GLN cc_start: 0.9299 (mt0) cc_final: 0.8776 (mp10) REVERT: D 164 TYR cc_start: 0.8946 (t80) cc_final: 0.8093 (t80) REVERT: D 171 THR cc_start: 0.9329 (m) cc_final: 0.9053 (p) REVERT: D 192 GLN cc_start: 0.8993 (tp40) cc_final: 0.8666 (tp-100) REVERT: G 55 MET cc_start: 0.9082 (mtp) cc_final: 0.8761 (mtp) REVERT: G 195 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8609 (p0) REVERT: H 51 ASP cc_start: 0.9007 (m-30) cc_final: 0.8320 (m-30) REVERT: H 67 GLN cc_start: 0.8880 (tp40) cc_final: 0.8575 (tp40) REVERT: H 144 MET cc_start: 0.8544 (ttm) cc_final: 0.7924 (ttm) REVERT: H 164 TYR cc_start: 0.8982 (t80) cc_final: 0.8613 (t80) REVERT: I 66 MET cc_start: 0.8616 (mmm) cc_final: 0.8225 (mmm) REVERT: I 76 GLU cc_start: 0.8731 (tp30) cc_final: 0.8223 (tp30) REVERT: I 114 GLN cc_start: 0.9351 (mt0) cc_final: 0.8930 (mp10) REVERT: J 164 TYR cc_start: 0.8940 (t80) cc_final: 0.8479 (t80) REVERT: P 44 SER cc_start: 0.8958 (m) cc_final: 0.8714 (p) REVERT: P 66 MET cc_start: 0.9050 (tpt) cc_final: 0.8761 (tpt) REVERT: P 109 SER cc_start: 0.7082 (OUTLIER) cc_final: 0.6699 (m) REVERT: P 185 MET cc_start: 0.9211 (mtm) cc_final: 0.8977 (ttm) REVERT: Q 51 ASP cc_start: 0.8932 (m-30) cc_final: 0.8405 (m-30) REVERT: R 35 GLU cc_start: 0.8835 (pt0) cc_final: 0.8155 (tt0) REVERT: R 76 GLU cc_start: 0.8849 (tp30) cc_final: 0.8363 (tp30) REVERT: R 114 GLN cc_start: 0.9315 (mt0) cc_final: 0.8787 (mp10) REVERT: S 164 TYR cc_start: 0.8967 (t80) cc_final: 0.8426 (t80) REVERT: V 109 SER cc_start: 0.7418 (OUTLIER) cc_final: 0.7062 (m) REVERT: V 195 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8469 (p0) REVERT: V 215 MET cc_start: 0.8622 (mtt) cc_final: 0.8379 (mtt) REVERT: W 51 ASP cc_start: 0.9012 (m-30) cc_final: 0.8470 (m-30) REVERT: W 55 MET cc_start: 0.9206 (ttt) cc_final: 0.8988 (tmm) REVERT: W 176 GLN cc_start: 0.8349 (mt0) cc_final: 0.8119 (mt0) REVERT: X 35 GLU cc_start: 0.8708 (pt0) cc_final: 0.8097 (tt0) REVERT: X 114 GLN cc_start: 0.9373 (mt0) cc_final: 0.8805 (mp10) REVERT: 0 164 TYR cc_start: 0.8989 (t80) cc_final: 0.8466 (t80) REVERT: 3 51 ASP cc_start: 0.9140 (m-30) cc_final: 0.8915 (m-30) outliers start: 77 outliers final: 59 residues processed: 474 average time/residue: 0.1423 time to fit residues: 109.3008 Evaluate side-chains 466 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 400 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 109 SER Chi-restraints excluded: chain R residue 32 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 195 ASN Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 149 SER Chi-restraints excluded: chain W residue 215 MET Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 150 ILE Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Chi-restraints excluded: chain 3 residue 71 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 278 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 117 optimal weight: 0.0770 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 GLN W 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.056973 restraints weight = 83702.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.058618 restraints weight = 50856.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.059706 restraints weight = 37753.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060380 restraints weight = 31425.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.060760 restraints weight = 28165.722| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 22690 Z= 0.118 Angle : 0.559 10.244 31140 Z= 0.277 Chirality : 0.039 0.203 3730 Planarity : 0.005 0.055 3980 Dihedral : 4.930 53.602 3179 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.04 % Allowed : 18.69 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.15), residues: 2985 helix: 1.70 (0.11), residues: 2100 sheet: None (None), residues: 0 loop : 1.07 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 82 TYR 0.029 0.001 TYR L 164 PHE 0.010 0.001 PHE L 40 TRP 0.011 0.001 TRP P 23 HIS 0.003 0.001 HIS P 62 Details of bonding type rmsd covalent geometry : bond 0.00274 (22690) covalent geometry : angle 0.55868 (31140) hydrogen bonds : bond 0.03791 ( 1420) hydrogen bonds : angle 3.97041 ( 4185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 460 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8897 (m-30) cc_final: 0.8317 (m-30) REVERT: L 55 MET cc_start: 0.9083 (tmm) cc_final: 0.8772 (tmm) REVERT: L 144 MET cc_start: 0.8669 (ttm) cc_final: 0.7651 (ttm) REVERT: L 215 MET cc_start: 0.8432 (mtp) cc_final: 0.8167 (mtp) REVERT: M 35 GLU cc_start: 0.8702 (pt0) cc_final: 0.8216 (tt0) REVERT: M 76 GLU cc_start: 0.8761 (tp30) cc_final: 0.8528 (tp30) REVERT: M 82 ARG cc_start: 0.8289 (tmm160) cc_final: 0.8036 (tmm160) REVERT: M 114 GLN cc_start: 0.9349 (mt0) cc_final: 0.8947 (mp10) REVERT: N 164 TYR cc_start: 0.8908 (t80) cc_final: 0.8300 (t80) REVERT: N 192 GLN cc_start: 0.8913 (tp40) cc_final: 0.8549 (tp-100) REVERT: N 215 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8564 (ttp) REVERT: A 51 ASP cc_start: 0.9163 (m-30) cc_final: 0.8881 (m-30) REVERT: A 57 ASN cc_start: 0.9062 (m-40) cc_final: 0.8458 (t0) REVERT: A 195 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8504 (p0) REVERT: B 51 ASP cc_start: 0.8860 (m-30) cc_final: 0.8226 (m-30) REVERT: B 55 MET cc_start: 0.9048 (tmm) cc_final: 0.8819 (tmm) REVERT: B 179 GLN cc_start: 0.8124 (tp40) cc_final: 0.7886 (mm-40) REVERT: C 32 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: C 35 GLU cc_start: 0.8694 (pt0) cc_final: 0.7968 (tt0) REVERT: C 76 GLU cc_start: 0.8737 (tp30) cc_final: 0.8266 (tp30) REVERT: C 114 GLN cc_start: 0.9332 (mt0) cc_final: 0.8873 (mp10) REVERT: D 164 TYR cc_start: 0.8911 (t80) cc_final: 0.8084 (t80) REVERT: D 171 THR cc_start: 0.9195 (m) cc_final: 0.8878 (p) REVERT: D 192 GLN cc_start: 0.8907 (tp40) cc_final: 0.8692 (tp-100) REVERT: G 57 ASN cc_start: 0.9006 (m-40) cc_final: 0.8481 (t0) REVERT: G 195 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8441 (p0) REVERT: H 51 ASP cc_start: 0.8979 (m-30) cc_final: 0.8359 (m-30) REVERT: H 144 MET cc_start: 0.8237 (ttm) cc_final: 0.7975 (ttp) REVERT: H 164 TYR cc_start: 0.8961 (t80) cc_final: 0.8641 (t80) REVERT: I 76 GLU cc_start: 0.8724 (tp30) cc_final: 0.8318 (tp30) REVERT: I 114 GLN cc_start: 0.9336 (mt0) cc_final: 0.8937 (mp10) REVERT: J 164 TYR cc_start: 0.8834 (t80) cc_final: 0.8448 (t80) REVERT: J 215 MET cc_start: 0.8707 (ttp) cc_final: 0.8339 (ttp) REVERT: P 44 SER cc_start: 0.8743 (m) cc_final: 0.8173 (p) REVERT: P 215 MET cc_start: 0.8626 (mtt) cc_final: 0.8386 (mtm) REVERT: Q 51 ASP cc_start: 0.8904 (m-30) cc_final: 0.8441 (m-30) REVERT: R 35 GLU cc_start: 0.8803 (pt0) cc_final: 0.8158 (tt0) REVERT: R 41 SER cc_start: 0.9163 (t) cc_final: 0.8950 (p) REVERT: R 76 GLU cc_start: 0.8826 (tp30) cc_final: 0.8356 (tp30) REVERT: R 114 GLN cc_start: 0.9345 (mt0) cc_final: 0.8916 (mp10) REVERT: S 164 TYR cc_start: 0.8929 (t80) cc_final: 0.8383 (t80) REVERT: V 57 ASN cc_start: 0.9051 (m-40) cc_final: 0.8458 (t0) REVERT: V 195 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8363 (p0) REVERT: W 51 ASP cc_start: 0.8944 (m-30) cc_final: 0.8393 (m-30) REVERT: X 35 GLU cc_start: 0.8644 (pt0) cc_final: 0.7995 (tt0) REVERT: X 114 GLN cc_start: 0.9316 (mt0) cc_final: 0.8740 (mp10) REVERT: 0 164 TYR cc_start: 0.8918 (t80) cc_final: 0.8438 (t80) REVERT: 3 51 ASP cc_start: 0.9165 (m-30) cc_final: 0.8963 (m-30) REVERT: 3 57 ASN cc_start: 0.8868 (m-40) cc_final: 0.8606 (t0) REVERT: 3 102 SER cc_start: 0.8964 (m) cc_final: 0.8638 (t) outliers start: 65 outliers final: 36 residues processed: 514 average time/residue: 0.1225 time to fit residues: 103.0257 Evaluate side-chains 455 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 414 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain R residue 32 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 195 ASN Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 27 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 275 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 chunk 277 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 63 GLN ** R 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 193 ASN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.075951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.056779 restraints weight = 83817.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.058400 restraints weight = 51443.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059443 restraints weight = 38414.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.060103 restraints weight = 32242.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060498 restraints weight = 28953.207| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22690 Z= 0.130 Angle : 0.589 12.975 31140 Z= 0.288 Chirality : 0.039 0.208 3730 Planarity : 0.005 0.057 3980 Dihedral : 4.740 53.992 3171 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.62 % Allowed : 19.86 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.15), residues: 2985 helix: 1.73 (0.11), residues: 2095 sheet: None (None), residues: 0 loop : 1.05 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 82 TYR 0.031 0.001 TYR L 164 PHE 0.016 0.001 PHE Z 321 TRP 0.009 0.001 TRP 3 23 HIS 0.003 0.000 HIS V 62 Details of bonding type rmsd covalent geometry : bond 0.00313 (22690) covalent geometry : angle 0.58884 (31140) hydrogen bonds : bond 0.03796 ( 1420) hydrogen bonds : angle 4.00591 ( 4185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 428 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9543 (ttmm) cc_final: 0.9326 (tppp) REVERT: L 51 ASP cc_start: 0.8879 (m-30) cc_final: 0.8294 (m-30) REVERT: L 144 MET cc_start: 0.8674 (ttm) cc_final: 0.7629 (ttm) REVERT: L 215 MET cc_start: 0.8517 (mtp) cc_final: 0.8262 (mtp) REVERT: M 35 GLU cc_start: 0.8706 (pt0) cc_final: 0.8243 (tt0) REVERT: M 76 GLU cc_start: 0.8786 (tp30) cc_final: 0.8577 (tp30) REVERT: M 82 ARG cc_start: 0.8224 (tmm160) cc_final: 0.7989 (tmm160) REVERT: M 114 GLN cc_start: 0.9349 (mt0) cc_final: 0.8958 (mp10) REVERT: N 164 TYR cc_start: 0.8926 (t80) cc_final: 0.8292 (t80) REVERT: N 192 GLN cc_start: 0.8913 (tp40) cc_final: 0.8551 (tp-100) REVERT: N 215 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8552 (ttp) REVERT: A 51 ASP cc_start: 0.9188 (m-30) cc_final: 0.8953 (m-30) REVERT: A 57 ASN cc_start: 0.9072 (m-40) cc_final: 0.8446 (t0) REVERT: A 195 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8468 (p0) REVERT: B 51 ASP cc_start: 0.8883 (m-30) cc_final: 0.8239 (m-30) REVERT: B 55 MET cc_start: 0.9089 (tmm) cc_final: 0.8834 (tmm) REVERT: C 32 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: C 35 GLU cc_start: 0.8660 (pt0) cc_final: 0.7927 (tt0) REVERT: C 76 GLU cc_start: 0.8699 (tp30) cc_final: 0.8241 (tp30) REVERT: C 114 GLN cc_start: 0.9340 (mt0) cc_final: 0.8943 (mp10) REVERT: D 171 THR cc_start: 0.9224 (m) cc_final: 0.8907 (p) REVERT: D 192 GLN cc_start: 0.9040 (tp40) cc_final: 0.8726 (tp-100) REVERT: D 215 MET cc_start: 0.9364 (ttm) cc_final: 0.8853 (ttm) REVERT: G 44 SER cc_start: 0.8788 (m) cc_final: 0.8141 (p) REVERT: G 55 MET cc_start: 0.9032 (mtp) cc_final: 0.8764 (mtm) REVERT: G 57 ASN cc_start: 0.8991 (m-40) cc_final: 0.8482 (t0) REVERT: G 144 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8638 (ttp) REVERT: G 195 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8424 (p0) REVERT: H 51 ASP cc_start: 0.9026 (m-30) cc_final: 0.8410 (m-30) REVERT: H 55 MET cc_start: 0.9022 (tmm) cc_final: 0.8799 (tmm) REVERT: H 66 MET cc_start: 0.8579 (tpp) cc_final: 0.8361 (mmm) REVERT: H 164 TYR cc_start: 0.8955 (t80) cc_final: 0.8658 (t80) REVERT: I 76 GLU cc_start: 0.8762 (tp30) cc_final: 0.8350 (tp30) REVERT: I 114 GLN cc_start: 0.9331 (mt0) cc_final: 0.8944 (mp10) REVERT: J 164 TYR cc_start: 0.8863 (t80) cc_final: 0.8445 (t80) REVERT: P 44 SER cc_start: 0.8753 (m) cc_final: 0.8165 (p) REVERT: Q 51 ASP cc_start: 0.8920 (m-30) cc_final: 0.8426 (m-30) REVERT: Q 143 ARG cc_start: 0.9254 (tpt90) cc_final: 0.8817 (tpm170) REVERT: R 35 GLU cc_start: 0.8806 (pt0) cc_final: 0.8073 (tt0) REVERT: R 76 GLU cc_start: 0.8822 (tp30) cc_final: 0.8381 (tp30) REVERT: R 114 GLN cc_start: 0.9361 (mt0) cc_final: 0.8952 (mp10) REVERT: S 164 TYR cc_start: 0.8959 (t80) cc_final: 0.8375 (t80) REVERT: S 215 MET cc_start: 0.8959 (ttm) cc_final: 0.8561 (ttp) REVERT: V 57 ASN cc_start: 0.9061 (m-40) cc_final: 0.8437 (t0) REVERT: V 195 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8399 (p0) REVERT: W 51 ASP cc_start: 0.8935 (m-30) cc_final: 0.8358 (m-30) REVERT: W 55 MET cc_start: 0.9032 (tmm) cc_final: 0.8803 (tmm) REVERT: X 35 GLU cc_start: 0.8652 (pt0) cc_final: 0.7939 (tt0) REVERT: 0 164 TYR cc_start: 0.8980 (t80) cc_final: 0.8443 (t80) REVERT: 3 102 SER cc_start: 0.8969 (m) cc_final: 0.8665 (t) outliers start: 56 outliers final: 38 residues processed: 474 average time/residue: 0.1251 time to fit residues: 97.1058 Evaluate side-chains 459 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 415 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 195 ASN Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Chi-restraints excluded: chain 3 residue 185 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 230 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 144 optimal weight: 0.6980 chunk 143 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.076306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.057168 restraints weight = 82587.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058788 restraints weight = 51046.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059824 restraints weight = 38206.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060471 restraints weight = 32126.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060877 restraints weight = 28909.089| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22690 Z= 0.129 Angle : 0.601 12.782 31140 Z= 0.292 Chirality : 0.039 0.213 3730 Planarity : 0.005 0.057 3980 Dihedral : 4.711 56.261 3169 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.30 % Allowed : 20.42 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.15), residues: 2985 helix: 1.73 (0.11), residues: 2095 sheet: None (None), residues: 0 loop : 1.06 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 82 TYR 0.031 0.001 TYR Q 164 PHE 0.019 0.001 PHE Z 321 TRP 0.008 0.001 TRP 3 23 HIS 0.005 0.001 HIS R 84 Details of bonding type rmsd covalent geometry : bond 0.00313 (22690) covalent geometry : angle 0.60134 (31140) hydrogen bonds : bond 0.03696 ( 1420) hydrogen bonds : angle 3.98130 ( 4185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 437 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9547 (ttmm) cc_final: 0.9327 (tppp) REVERT: L 51 ASP cc_start: 0.8895 (m-30) cc_final: 0.8320 (m-30) REVERT: L 55 MET cc_start: 0.9053 (tmm) cc_final: 0.8829 (tmm) REVERT: L 143 ARG cc_start: 0.9223 (tpt90) cc_final: 0.8914 (tpm170) REVERT: L 144 MET cc_start: 0.8645 (ttm) cc_final: 0.7549 (ttm) REVERT: L 164 TYR cc_start: 0.8329 (t80) cc_final: 0.8062 (t80) REVERT: L 215 MET cc_start: 0.8537 (mtp) cc_final: 0.8293 (mtp) REVERT: M 35 GLU cc_start: 0.8704 (pt0) cc_final: 0.8238 (tt0) REVERT: M 114 GLN cc_start: 0.9350 (mt0) cc_final: 0.8960 (mp10) REVERT: N 164 TYR cc_start: 0.8918 (t80) cc_final: 0.8287 (t80) REVERT: N 192 GLN cc_start: 0.8913 (tp40) cc_final: 0.8547 (tp-100) REVERT: N 205 LEU cc_start: 0.8918 (tp) cc_final: 0.8703 (tt) REVERT: N 215 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8558 (ttp) REVERT: A 51 ASP cc_start: 0.9181 (m-30) cc_final: 0.8967 (m-30) REVERT: A 57 ASN cc_start: 0.9068 (m-40) cc_final: 0.8449 (t0) REVERT: A 185 MET cc_start: 0.8759 (mtp) cc_final: 0.8471 (mtp) REVERT: A 195 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8441 (p0) REVERT: B 51 ASP cc_start: 0.8849 (m-30) cc_final: 0.8238 (m-30) REVERT: B 55 MET cc_start: 0.9103 (tmm) cc_final: 0.8818 (tmm) REVERT: C 32 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: C 35 GLU cc_start: 0.8657 (pt0) cc_final: 0.7954 (tt0) REVERT: C 66 MET cc_start: 0.8667 (mmm) cc_final: 0.8258 (mmm) REVERT: C 76 GLU cc_start: 0.8723 (tp30) cc_final: 0.8397 (tp30) REVERT: C 114 GLN cc_start: 0.9335 (mt0) cc_final: 0.8956 (mp10) REVERT: D 171 THR cc_start: 0.9241 (m) cc_final: 0.8906 (p) REVERT: D 192 GLN cc_start: 0.9047 (tp40) cc_final: 0.8737 (tp-100) REVERT: D 215 MET cc_start: 0.9360 (ttm) cc_final: 0.8858 (ttm) REVERT: G 44 SER cc_start: 0.8820 (m) cc_final: 0.8148 (p) REVERT: G 55 MET cc_start: 0.9114 (mtp) cc_final: 0.8749 (mtm) REVERT: G 57 ASN cc_start: 0.9000 (m-40) cc_final: 0.8471 (t0) REVERT: G 144 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8646 (ttp) REVERT: H 51 ASP cc_start: 0.8994 (m-30) cc_final: 0.8378 (m-30) REVERT: H 55 MET cc_start: 0.9011 (tmm) cc_final: 0.8754 (tmm) REVERT: H 179 GLN cc_start: 0.7580 (tp40) cc_final: 0.7239 (tp40) REVERT: I 76 GLU cc_start: 0.8736 (tp30) cc_final: 0.8342 (tp30) REVERT: I 114 GLN cc_start: 0.9357 (mt0) cc_final: 0.8969 (mp10) REVERT: J 164 TYR cc_start: 0.8836 (t80) cc_final: 0.8442 (t80) REVERT: P 44 SER cc_start: 0.8774 (m) cc_final: 0.8206 (p) REVERT: Q 51 ASP cc_start: 0.8941 (m-30) cc_final: 0.8451 (m-30) REVERT: Q 215 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8100 (mtt) REVERT: R 35 GLU cc_start: 0.8790 (pt0) cc_final: 0.8055 (tt0) REVERT: R 76 GLU cc_start: 0.8806 (tp30) cc_final: 0.8386 (tp30) REVERT: R 102 SER cc_start: 0.8877 (t) cc_final: 0.8414 (t) REVERT: R 114 GLN cc_start: 0.9354 (mt0) cc_final: 0.8987 (mp10) REVERT: S 164 TYR cc_start: 0.8974 (t80) cc_final: 0.8370 (t80) REVERT: S 215 MET cc_start: 0.9004 (ttm) cc_final: 0.8611 (ttp) REVERT: V 57 ASN cc_start: 0.9056 (m-40) cc_final: 0.8444 (t0) REVERT: V 144 MET cc_start: 0.8935 (ttp) cc_final: 0.8618 (ttp) REVERT: W 51 ASP cc_start: 0.8941 (m-30) cc_final: 0.8361 (m-30) REVERT: W 55 MET cc_start: 0.9081 (tmm) cc_final: 0.8826 (tmm) REVERT: X 35 GLU cc_start: 0.8620 (pt0) cc_final: 0.7912 (tt0) REVERT: 0 164 TYR cc_start: 0.8989 (t80) cc_final: 0.8446 (t80) REVERT: 0 218 CYS cc_start: 0.8016 (t) cc_final: 0.7687 (t) REVERT: 3 57 ASN cc_start: 0.8786 (m-40) cc_final: 0.8423 (t0) REVERT: 3 66 MET cc_start: 0.8915 (tpt) cc_final: 0.8415 (tpt) REVERT: 3 102 SER cc_start: 0.8960 (m) cc_final: 0.8648 (t) outliers start: 49 outliers final: 38 residues processed: 477 average time/residue: 0.1402 time to fit residues: 108.8475 Evaluate side-chains 467 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 424 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain Q residue 215 MET Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Chi-restraints excluded: chain 3 residue 185 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 96 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.055498 restraints weight = 83679.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.057066 restraints weight = 52073.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.058085 restraints weight = 39154.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.058712 restraints weight = 32909.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.059089 restraints weight = 29723.129| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 22690 Z= 0.191 Angle : 0.647 12.481 31140 Z= 0.320 Chirality : 0.041 0.217 3730 Planarity : 0.005 0.058 3980 Dihedral : 4.849 58.236 3169 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.44 % Allowed : 20.94 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.15), residues: 2985 helix: 1.64 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : 0.97 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 82 TYR 0.037 0.002 TYR Q 164 PHE 0.025 0.002 PHE Z 321 TRP 0.007 0.001 TRP C 80 HIS 0.004 0.001 HIS Q 84 Details of bonding type rmsd covalent geometry : bond 0.00460 (22690) covalent geometry : angle 0.64709 (31140) hydrogen bonds : bond 0.04070 ( 1420) hydrogen bonds : angle 4.23067 ( 4185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 431 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8925 (m-30) cc_final: 0.8358 (m-30) REVERT: L 55 MET cc_start: 0.9094 (tmm) cc_final: 0.8865 (tmm) REVERT: L 143 ARG cc_start: 0.9228 (tpt90) cc_final: 0.8660 (tpm170) REVERT: L 144 MET cc_start: 0.8640 (ttm) cc_final: 0.7661 (ttm) REVERT: L 164 TYR cc_start: 0.8528 (t80) cc_final: 0.8249 (t80) REVERT: L 215 MET cc_start: 0.8660 (mtp) cc_final: 0.8445 (mtp) REVERT: M 35 GLU cc_start: 0.8705 (pt0) cc_final: 0.8283 (tt0) REVERT: M 76 GLU cc_start: 0.8586 (tp30) cc_final: 0.8367 (tp30) REVERT: M 114 GLN cc_start: 0.9357 (mt0) cc_final: 0.8961 (mp10) REVERT: N 164 TYR cc_start: 0.8946 (t80) cc_final: 0.8249 (t80) REVERT: N 192 GLN cc_start: 0.8963 (tp40) cc_final: 0.8707 (tp-100) REVERT: N 205 LEU cc_start: 0.8938 (tp) cc_final: 0.8724 (tt) REVERT: N 215 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8445 (ttp) REVERT: A 51 ASP cc_start: 0.9176 (m-30) cc_final: 0.8915 (m-30) REVERT: B 51 ASP cc_start: 0.8911 (m-30) cc_final: 0.8308 (m-30) REVERT: C 32 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: C 35 GLU cc_start: 0.8715 (pt0) cc_final: 0.7991 (tt0) REVERT: C 76 GLU cc_start: 0.8734 (tp30) cc_final: 0.8295 (tp30) REVERT: C 114 GLN cc_start: 0.9366 (mt0) cc_final: 0.8983 (mp10) REVERT: D 171 THR cc_start: 0.9331 (m) cc_final: 0.9059 (p) REVERT: D 192 GLN cc_start: 0.9078 (tp40) cc_final: 0.8771 (tp-100) REVERT: G 44 SER cc_start: 0.8984 (m) cc_final: 0.8403 (p) REVERT: H 44 SER cc_start: 0.9049 (p) cc_final: 0.8765 (p) REVERT: H 51 ASP cc_start: 0.9001 (m-30) cc_final: 0.8379 (m-30) REVERT: H 164 TYR cc_start: 0.8813 (t80) cc_final: 0.8500 (t80) REVERT: I 76 GLU cc_start: 0.8730 (tp30) cc_final: 0.8241 (tp30) REVERT: I 114 GLN cc_start: 0.9319 (mt0) cc_final: 0.8948 (mp10) REVERT: J 164 TYR cc_start: 0.8882 (t80) cc_final: 0.8404 (t80) REVERT: P 44 SER cc_start: 0.8964 (m) cc_final: 0.8419 (p) REVERT: Q 51 ASP cc_start: 0.8951 (m-30) cc_final: 0.8442 (m-30) REVERT: Q 143 ARG cc_start: 0.9278 (tpt90) cc_final: 0.8904 (tpm170) REVERT: Q 215 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8066 (mtt) REVERT: R 35 GLU cc_start: 0.8823 (pt0) cc_final: 0.7998 (tp30) REVERT: R 76 GLU cc_start: 0.8789 (tp30) cc_final: 0.8342 (tp30) REVERT: R 114 GLN cc_start: 0.9350 (mt0) cc_final: 0.8956 (mp10) REVERT: S 164 TYR cc_start: 0.9023 (t80) cc_final: 0.8419 (t80) REVERT: V 57 ASN cc_start: 0.9081 (m-40) cc_final: 0.8435 (t0) REVERT: W 51 ASP cc_start: 0.8936 (m-30) cc_final: 0.8332 (m-30) REVERT: X 35 GLU cc_start: 0.8655 (pt0) cc_final: 0.7949 (tt0) REVERT: 0 164 TYR cc_start: 0.9043 (t80) cc_final: 0.8486 (t80) REVERT: 0 215 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8971 (ttp) REVERT: 0 218 CYS cc_start: 0.7952 (t) cc_final: 0.7699 (t) REVERT: 3 44 SER cc_start: 0.8980 (m) cc_final: 0.8530 (p) REVERT: 3 102 SER cc_start: 0.8975 (m) cc_final: 0.8675 (t) outliers start: 52 outliers final: 41 residues processed: 473 average time/residue: 0.1360 time to fit residues: 105.5220 Evaluate side-chains 464 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 419 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 193 ASN Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain Q residue 215 MET Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 0 residue 215 MET Chi-restraints excluded: chain 1 residue 315 LEU Chi-restraints excluded: chain 2 residue 319 GLN Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Chi-restraints excluded: chain 3 residue 185 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 55 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 87 optimal weight: 30.0000 chunk 146 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 281 optimal weight: 0.0040 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 285 optimal weight: 8.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.056643 restraints weight = 83293.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.058245 restraints weight = 51673.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.059284 restraints weight = 38823.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059935 restraints weight = 32625.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060323 restraints weight = 29380.719| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 22690 Z= 0.140 Angle : 0.636 11.146 31140 Z= 0.311 Chirality : 0.040 0.237 3730 Planarity : 0.005 0.059 3980 Dihedral : 4.673 57.395 3165 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.30 % Allowed : 21.97 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.15), residues: 2985 helix: 1.65 (0.11), residues: 2125 sheet: None (None), residues: 0 loop : 1.04 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 82 TYR 0.034 0.002 TYR Q 164 PHE 0.023 0.001 PHE Z 321 TRP 0.010 0.001 TRP J 184 HIS 0.002 0.000 HIS V 62 Details of bonding type rmsd covalent geometry : bond 0.00346 (22690) covalent geometry : angle 0.63648 (31140) hydrogen bonds : bond 0.03874 ( 1420) hydrogen bonds : angle 4.09413 ( 4185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 433 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9541 (ttmm) cc_final: 0.9318 (tppp) REVERT: L 51 ASP cc_start: 0.8919 (m-30) cc_final: 0.8364 (m-30) REVERT: L 55 MET cc_start: 0.9055 (tmm) cc_final: 0.8811 (tmm) REVERT: L 143 ARG cc_start: 0.9175 (tpt90) cc_final: 0.8635 (tpm170) REVERT: L 144 MET cc_start: 0.8633 (ttm) cc_final: 0.7584 (ttm) REVERT: L 164 TYR cc_start: 0.8495 (t80) cc_final: 0.8215 (t80) REVERT: M 35 GLU cc_start: 0.8701 (pt0) cc_final: 0.8205 (tt0) REVERT: M 76 GLU cc_start: 0.8608 (tp30) cc_final: 0.8400 (tp30) REVERT: M 114 GLN cc_start: 0.9353 (mt0) cc_final: 0.8952 (mp10) REVERT: N 164 TYR cc_start: 0.8933 (t80) cc_final: 0.8301 (t80) REVERT: N 192 GLN cc_start: 0.8879 (tp40) cc_final: 0.8483 (tp-100) REVERT: N 205 LEU cc_start: 0.8929 (tp) cc_final: 0.8724 (tt) REVERT: N 215 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8404 (ttp) REVERT: A 45 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 51 ASP cc_start: 0.9168 (m-30) cc_final: 0.8903 (m-30) REVERT: B 51 ASP cc_start: 0.8884 (m-30) cc_final: 0.8289 (m-30) REVERT: B 55 MET cc_start: 0.9073 (tmm) cc_final: 0.8857 (tmm) REVERT: C 32 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: C 35 GLU cc_start: 0.8641 (pt0) cc_final: 0.7948 (tt0) REVERT: C 76 GLU cc_start: 0.8718 (tp30) cc_final: 0.8316 (tp30) REVERT: C 114 GLN cc_start: 0.9364 (mt0) cc_final: 0.8979 (mp10) REVERT: D 171 THR cc_start: 0.9267 (m) cc_final: 0.8991 (p) REVERT: D 192 GLN cc_start: 0.9050 (tp40) cc_final: 0.8746 (tp-100) REVERT: G 13 GLN cc_start: 0.8868 (tp-100) cc_final: 0.8584 (tm-30) REVERT: G 44 SER cc_start: 0.8812 (m) cc_final: 0.8118 (p) REVERT: G 55 MET cc_start: 0.9079 (mtp) cc_final: 0.8854 (mtp) REVERT: G 57 ASN cc_start: 0.9071 (m-40) cc_final: 0.8479 (t0) REVERT: H 51 ASP cc_start: 0.8991 (m-30) cc_final: 0.8373 (m-30) REVERT: H 55 MET cc_start: 0.9029 (tmm) cc_final: 0.8826 (tmm) REVERT: H 164 TYR cc_start: 0.8769 (t80) cc_final: 0.8440 (t80) REVERT: I 76 GLU cc_start: 0.8699 (tp30) cc_final: 0.8229 (tp30) REVERT: I 114 GLN cc_start: 0.9305 (mt0) cc_final: 0.8925 (mp10) REVERT: J 164 TYR cc_start: 0.8942 (t80) cc_final: 0.8518 (t80) REVERT: P 44 SER cc_start: 0.8837 (m) cc_final: 0.8249 (p) REVERT: Q 51 ASP cc_start: 0.8950 (m-30) cc_final: 0.8457 (m-30) REVERT: Q 143 ARG cc_start: 0.9249 (tpt90) cc_final: 0.8881 (tpm170) REVERT: R 35 GLU cc_start: 0.8766 (pt0) cc_final: 0.8033 (tt0) REVERT: R 76 GLU cc_start: 0.8754 (tp30) cc_final: 0.8340 (tp30) REVERT: R 102 SER cc_start: 0.8904 (t) cc_final: 0.8443 (t) REVERT: R 114 GLN cc_start: 0.9359 (mt0) cc_final: 0.8987 (mp10) REVERT: S 164 TYR cc_start: 0.8978 (t80) cc_final: 0.8398 (t80) REVERT: S 215 MET cc_start: 0.8863 (ttm) cc_final: 0.8465 (ttp) REVERT: V 57 ASN cc_start: 0.9058 (m-40) cc_final: 0.8443 (t0) REVERT: W 51 ASP cc_start: 0.8921 (m-30) cc_final: 0.8335 (m-30) REVERT: W 55 MET cc_start: 0.9023 (tmm) cc_final: 0.8804 (tmm) REVERT: X 35 GLU cc_start: 0.8636 (pt0) cc_final: 0.7936 (tt0) REVERT: 0 164 TYR cc_start: 0.9006 (t80) cc_final: 0.8467 (t80) REVERT: 0 215 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8875 (ttp) REVERT: 3 44 SER cc_start: 0.8868 (m) cc_final: 0.8330 (p) REVERT: 3 57 ASN cc_start: 0.8817 (m-40) cc_final: 0.8442 (t0) REVERT: 3 102 SER cc_start: 0.8962 (m) cc_final: 0.8672 (t) outliers start: 49 outliers final: 40 residues processed: 474 average time/residue: 0.1260 time to fit residues: 97.3613 Evaluate side-chains 466 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 423 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 0 residue 215 MET Chi-restraints excluded: chain 2 residue 319 GLN Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Chi-restraints excluded: chain 3 residue 185 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 90 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 104 optimal weight: 0.0670 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 ASN J 219 GLN P 62 HIS S 219 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 62 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.077185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.058051 restraints weight = 83539.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.059708 restraints weight = 51367.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060806 restraints weight = 38274.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.061462 restraints weight = 31951.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.061878 restraints weight = 28713.739| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22690 Z= 0.122 Angle : 0.624 10.743 31140 Z= 0.303 Chirality : 0.039 0.241 3730 Planarity : 0.005 0.058 3980 Dihedral : 4.568 56.953 3165 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.11 % Allowed : 22.20 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.16), residues: 2985 helix: 1.74 (0.11), residues: 2125 sheet: None (None), residues: 0 loop : 1.08 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 82 TYR 0.028 0.001 TYR H 164 PHE 0.021 0.001 PHE Z 321 TRP 0.013 0.001 TRP 3 23 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00300 (22690) covalent geometry : angle 0.62420 (31140) hydrogen bonds : bond 0.03518 ( 1420) hydrogen bonds : angle 3.94713 ( 4185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4048.75 seconds wall clock time: 70 minutes 30.45 seconds (4230.45 seconds total)