Starting phenix.real_space_refine on Thu Jun 19 00:51:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejl_28186/06_2025/8ejl_28186.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejl_28186/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejl_28186/06_2025/8ejl_28186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejl_28186/06_2025/8ejl_28186.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejl_28186/06_2025/8ejl_28186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejl_28186/06_2025/8ejl_28186.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22155 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" 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, 'GLU:plan': 13, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "C" 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 Chain: "0" 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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "1" 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: "2" 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: "3" 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, 'GLU:plan': 5, 'ARG:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Restraints were copied for chains: H, L, Q, W, E, K, T, Y, D, J, N, S, A, G, P, V, F, O, U, Z, I, M, R, X Time building chain proxies: 8.55, per 1000 atoms: 0.39 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: 6.50 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 2.31 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: 6.67 Time building geometry restraints manager: 7.65 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: 0.20 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'L' selection = chain 'Q' selection = chain 'W' } ncs_group { reference = chain '1' selection = chain 'E' selection = chain 'K' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain '0' selection = chain 'D' selection = chain 'J' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain '3' selection = chain 'A' selection = chain 'G' selection = chain 'P' selection = chain 'V' } ncs_group { reference = chain '2' selection = chain 'F' selection = chain 'O' selection = chain 'U' selection = chain 'Z' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'M' selection = chain 'R' selection = chain 'X' } 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 47.870 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP D 184 HIS 0.002 0.001 HIS I 120 PHE 0.008 0.002 PHE W 168 TYR 0.008 0.001 TYR G 145 ARG 0.003 0.001 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.20883 ( 1420) hydrogen bonds : angle 6.73311 ( 4185) covalent geometry : bond 0.00510 (22690) covalent geometry : angle 0.54490 (31140) *********************** 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 : 2.743 Fit side-chains 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: 0.8416 (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: 0.8795 (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: 0.8298 (tp40) REVERT: B 84 HIS cc_start: 0.8443 (m90) cc_final: 0.8083 (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: 0.7462 (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: 0.8163 (t80) REVERT: D 171 THR cc_start: 0.9396 (m) cc_final: 0.9113 (p) REVERT: D 214 MET cc_start: 0.9125 (mtp) cc_final: 0.8880 (mtt) 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: 0.8470 (m-30) REVERT: Q 67 GLN cc_start: 0.8812 (tp40) cc_final: 0.8529 (tp40) REVERT: Q 84 HIS cc_start: 0.8504 (m90) cc_final: 0.8060 (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: 0.8815 (mtm) REVERT: V 144 MET cc_start: 0.9051 (ttm) cc_final: 0.8784 (ttm) REVERT: W 51 ASP cc_start: 0.8998 (m-30) cc_final: 0.8505 (m-30) REVERT: W 67 GLN cc_start: 0.8824 (tp40) cc_final: 0.8460 (tp40) 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: 0.2985 time to fit residues: 278.6811 Evaluate side-chains 426 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 388 time to evaluate : 2.534 ------------------------------------------------------------------------------- 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 253 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.074668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.055592 restraints weight = 82924.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.057223 restraints weight = 50963.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058286 restraints weight = 37790.503| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 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 = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22690 Z= 0.172 Angle : 0.580 7.172 31140 Z= 0.301 Chirality : 0.041 0.182 3730 Planarity : 0.005 0.050 3980 Dihedral : 6.133 56.569 3213 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.45 % Allowed : 13.16 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.15), residues: 2985 helix: 1.61 (0.11), residues: 2125 sheet: None (None), residues: 0 loop : 0.90 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 133 HIS 0.004 0.001 HIS M 62 PHE 0.014 0.001 PHE G 161 TYR 0.022 0.002 TYR L 164 ARG 0.011 0.001 ARG H 82 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 1420) hydrogen bonds : angle 4.61866 ( 4185) covalent geometry : bond 0.00397 (22690) covalent geometry : angle 0.58031 (31140) *********************** 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 605 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 510 time to evaluate : 2.803 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: 0.8961 (m-30) cc_final: 0.8401 (m-30) REVERT: L 55 MET cc_start: 0.9171 (ttp) cc_final: 0.8902 (tmm) REVERT: L 117 TRP cc_start: 0.8552 (OUTLIER) cc_final: 0.8138 (m-90) REVERT: L 143 ARG cc_start: 0.9163 (tpt90) cc_final: 0.8334 (tpm170) REVERT: L 144 MET cc_start: 0.8821 (ttm) cc_final: 0.8329 (ttm) REVERT: L 176 GLN cc_start: 0.8014 (mt0) cc_final: 0.7744 (mt0) REVERT: L 214 MET cc_start: 0.9115 (mtm) cc_final: 0.8865 (mtp) REVERT: M 35 GLU cc_start: 0.8729 (pt0) cc_final: 0.8333 (tt0) REVERT: M 76 GLU cc_start: 0.8594 (tp30) cc_final: 0.8365 (tp30) REVERT: N 164 TYR cc_start: 0.8972 (t80) cc_final: 0.8354 (t80) REVERT: N 192 GLN cc_start: 0.8921 (tp40) cc_final: 0.8555 (tp-100) REVERT: A 45 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8495 (tm-30) REVERT: A 51 ASP cc_start: 0.9186 (m-30) cc_final: 0.8944 (m-30) REVERT: B 67 GLN cc_start: 0.8677 (tp40) cc_final: 0.8371 (tp40) REVERT: B 117 TRP cc_start: 0.8385 (OUTLIER) cc_final: 0.8056 (m-90) REVERT: C 32 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: C 35 GLU cc_start: 0.8891 (pt0) cc_final: 0.8307 (tt0) REVERT: C 39 MET cc_start: 0.9220 (tpp) cc_final: 0.8665 (mmm) REVERT: C 76 GLU cc_start: 0.8638 (tp30) cc_final: 0.8314 (tp30) REVERT: C 114 GLN cc_start: 0.9180 (mt0) cc_final: 0.8417 (mp-120) REVERT: D 164 TYR cc_start: 0.8899 (t80) cc_final: 0.8069 (t80) REVERT: D 171 THR cc_start: 0.9318 (m) cc_final: 0.9012 (p) REVERT: D 192 GLN cc_start: 0.8936 (tp40) cc_final: 0.8690 (tp-100) REVERT: G 29 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7963 (mt-10) REVERT: G 55 MET cc_start: 0.9089 (mtp) cc_final: 0.8771 (mtp) REVERT: G 109 SER cc_start: 0.7113 (OUTLIER) cc_final: 0.6890 (m) REVERT: G 185 MET cc_start: 0.9080 (mtt) cc_final: 0.8871 (mtm) REVERT: H 51 ASP cc_start: 0.9089 (m-30) cc_final: 0.8400 (m-30) REVERT: H 67 GLN cc_start: 0.8789 (tp40) cc_final: 0.8474 (tp40) REVERT: H 84 HIS cc_start: 0.8268 (m90) cc_final: 0.8002 (m90) REVERT: H 117 TRP cc_start: 0.8584 (OUTLIER) cc_final: 0.8358 (m-90) REVERT: I 35 GLU cc_start: 0.8634 (pt0) cc_final: 0.8209 (tp30) REVERT: I 39 MET cc_start: 0.8902 (tpp) cc_final: 0.8395 (mmm) REVERT: I 114 GLN cc_start: 0.9283 (mt0) cc_final: 0.8603 (mp10) REVERT: J 164 TYR cc_start: 0.8902 (t80) cc_final: 0.8534 (t80) REVERT: P 66 MET cc_start: 0.9068 (tpt) cc_final: 0.8828 (tpt) REVERT: P 109 SER cc_start: 0.7133 (OUTLIER) cc_final: 0.6849 (m) REVERT: P 195 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8911 (p0) REVERT: P 215 MET cc_start: 0.8818 (mtt) cc_final: 0.8547 (mtt) REVERT: Q 51 ASP cc_start: 0.8865 (m-30) cc_final: 0.8300 (m-30) REVERT: Q 67 GLN cc_start: 0.8792 (tp40) cc_final: 0.8494 (tp40) REVERT: Q 79 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8314 (mm-30) REVERT: Q 179 GLN cc_start: 0.7881 (tp40) cc_final: 0.7090 (tp40) REVERT: R 35 GLU cc_start: 0.8933 (pt0) cc_final: 0.8086 (tp30) REVERT: R 76 GLU cc_start: 0.8721 (tp30) cc_final: 0.8423 (tp30) REVERT: R 114 GLN cc_start: 0.9345 (mt0) cc_final: 0.8677 (mp10) REVERT: S 164 TYR cc_start: 0.8966 (t80) cc_final: 0.8274 (t80) REVERT: S 214 MET cc_start: 0.9009 (mtp) cc_final: 0.8793 (mtt) REVERT: V 109 SER cc_start: 0.7393 (OUTLIER) cc_final: 0.7059 (m) REVERT: V 195 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8877 (p0) REVERT: V 215 MET cc_start: 0.8847 (mtt) cc_final: 0.8471 (mtt) REVERT: W 51 ASP cc_start: 0.8983 (m-30) cc_final: 0.8477 (m-30) REVERT: W 67 GLN cc_start: 0.8686 (tp40) cc_final: 0.8318 (tp40) REVERT: X 35 GLU cc_start: 0.8732 (pt0) cc_final: 0.8013 (tt0) REVERT: X 114 GLN cc_start: 0.9306 (mt0) cc_final: 0.8624 (mp10) REVERT: 0 164 TYR cc_start: 0.8940 (t80) cc_final: 0.8413 (t80) REVERT: 3 51 ASP cc_start: 0.9157 (m-30) cc_final: 0.8866 (m-30) REVERT: 3 66 MET cc_start: 0.8907 (tpt) cc_final: 0.8398 (tpp) REVERT: 3 128 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7799 (tm-30) REVERT: 3 195 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8840 (p0) outliers start: 95 outliers final: 61 residues processed: 571 average time/residue: 0.3190 time to fit residues: 289.6596 Evaluate side-chains 474 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 403 time to evaluate : 2.522 ------------------------------------------------------------------------------- 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 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 129 ILE 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 150 ILE 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 33 SER Chi-restraints excluded: chain C residue 110 THR 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 G residue 16 SER Chi-restraints excluded: chain G residue 109 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 H residue 117 TRP Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 129 ILE 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 16 SER Chi-restraints excluded: chain P residue 109 SER Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 37 ILE 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 59 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 150 ILE Chi-restraints excluded: chain V residue 195 ASN Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 56 LEU 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 X residue 129 ILE Chi-restraints excluded: chain X residue 144 MET Chi-restraints excluded: chain 0 residue 150 ILE Chi-restraints excluded: chain 0 residue 151 LEU Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 3 residue 16 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 281 optimal weight: 0.0000 chunk 169 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 220 optimal weight: 0.2980 chunk 144 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 overall best weight: 1.4590 ------------------------------------------------------------------------------- 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 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 GLN ** 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 219 GLN V 112 GLN V 195 ASN X 21 ASN 0 219 GLN 2 319 GLN 3 195 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.056779 restraints weight = 81383.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.058413 restraints weight = 49579.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059478 restraints weight = 36756.388| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 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 = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2457 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= 0.124 Angle : 0.555 8.840 31140 Z= 0.280 Chirality : 0.040 0.214 3730 Planarity : 0.005 0.051 3980 Dihedral : 5.446 56.494 3202 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.61 % Allowed : 15.32 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.15), residues: 2985 helix: 1.74 (0.11), residues: 2090 sheet: None (None), residues: 0 loop : 1.08 (0.22), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 23 HIS 0.005 0.001 HIS M 84 PHE 0.009 0.001 PHE V 40 TYR 0.019 0.001 TYR L 164 ARG 0.009 0.001 ARG R 82 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 1420) hydrogen bonds : angle 4.16004 ( 4185) covalent geometry : bond 0.00278 (22690) covalent geometry : angle 0.55540 (31140) *********************** 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 533 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 456 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8931 (m-30) cc_final: 0.8359 (m-30) REVERT: L 144 MET cc_start: 0.8792 (ttm) cc_final: 0.8573 (ttm) REVERT: L 214 MET cc_start: 0.9047 (mtm) cc_final: 0.8739 (mtp) REVERT: M 35 GLU cc_start: 0.8773 (pt0) cc_final: 0.8256 (tt0) REVERT: M 76 GLU cc_start: 0.8593 (tp30) cc_final: 0.8287 (tp30) REVERT: N 164 TYR cc_start: 0.8954 (t80) cc_final: 0.8357 (t80) REVERT: N 192 GLN cc_start: 0.8914 (tp40) cc_final: 0.8559 (tp-100) REVERT: A 215 MET cc_start: 0.8857 (mtp) cc_final: 0.8558 (mtt) REVERT: B 51 ASP cc_start: 0.8942 (m-30) cc_final: 0.8299 (m-30) REVERT: B 215 MET cc_start: 0.8788 (ttm) cc_final: 0.8552 (mtp) REVERT: C 32 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: C 35 GLU cc_start: 0.8773 (pt0) cc_final: 0.8148 (tt0) REVERT: C 76 GLU cc_start: 0.8696 (tp30) cc_final: 0.8298 (tp30) REVERT: C 114 GLN cc_start: 0.9249 (mt0) cc_final: 0.8570 (mp10) REVERT: D 164 TYR cc_start: 0.8883 (t80) cc_final: 0.8033 (t80) REVERT: D 171 THR cc_start: 0.9248 (m) cc_final: 0.8914 (p) REVERT: D 192 GLN cc_start: 0.8951 (tp40) cc_final: 0.8699 (tp-100) REVERT: G 55 MET cc_start: 0.9025 (mtp) cc_final: 0.8799 (mtp) REVERT: H 51 ASP cc_start: 0.9063 (m-30) cc_final: 0.8399 (m-30) REVERT: H 143 ARG cc_start: 0.9163 (tpt90) cc_final: 0.8932 (tpt90) REVERT: I 76 GLU cc_start: 0.8666 (tp30) cc_final: 0.8117 (tp30) REVERT: I 82 ARG cc_start: 0.8277 (tmm160) cc_final: 0.8024 (ttp80) REVERT: I 114 GLN cc_start: 0.9365 (mt0) cc_final: 0.8764 (mp10) REVERT: J 164 TYR cc_start: 0.8884 (t80) cc_final: 0.8549 (t80) REVERT: P 66 MET cc_start: 0.9032 (tpt) cc_final: 0.8772 (tpt) REVERT: P 215 MET cc_start: 0.8589 (mtt) cc_final: 0.8328 (mtt) REVERT: Q 51 ASP cc_start: 0.8932 (m-30) cc_final: 0.8408 (m-30) REVERT: Q 144 MET cc_start: 0.8658 (ttm) cc_final: 0.8120 (ttm) REVERT: Q 179 GLN cc_start: 0.7860 (tp40) cc_final: 0.7186 (tp40) REVERT: R 35 GLU cc_start: 0.8793 (pt0) cc_final: 0.8009 (tt0) REVERT: R 41 SER cc_start: 0.9183 (t) cc_final: 0.8976 (p) REVERT: R 66 MET cc_start: 0.8763 (mmm) cc_final: 0.8497 (mmm) REVERT: R 76 GLU cc_start: 0.8754 (tp30) cc_final: 0.8439 (tp30) REVERT: R 114 GLN cc_start: 0.9303 (mt0) cc_final: 0.8687 (mp10) REVERT: S 164 TYR cc_start: 0.8951 (t80) cc_final: 0.8307 (t80) REVERT: S 214 MET cc_start: 0.9024 (mtp) cc_final: 0.8812 (mtt) REVERT: W 51 ASP cc_start: 0.8994 (m-30) cc_final: 0.8471 (m-30) REVERT: W 67 GLN cc_start: 0.8679 (tp40) cc_final: 0.8267 (tp40) REVERT: W 185 MET cc_start: 0.8818 (mtm) cc_final: 0.8225 (mtp) REVERT: X 35 GLU cc_start: 0.8747 (pt0) cc_final: 0.8035 (tt0) REVERT: X 66 MET cc_start: 0.8744 (mmm) cc_final: 0.8529 (mmm) REVERT: X 114 GLN cc_start: 0.9348 (mt0) cc_final: 0.8718 (mp10) REVERT: 0 164 TYR cc_start: 0.8935 (t80) cc_final: 0.8439 (t80) REVERT: 3 66 MET cc_start: 0.8887 (tpt) cc_final: 0.8356 (tpp) outliers start: 77 outliers final: 38 residues processed: 510 average time/residue: 0.3530 time to fit residues: 288.6581 Evaluate side-chains 452 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 413 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 32 PHE 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 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE 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 35 GLU Chi-restraints excluded: chain G residue 149 SER 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 J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain Q residue 37 ILE 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 16 SER Chi-restraints excluded: chain V residue 59 VAL 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 0 residue 210 THR Chi-restraints excluded: chain 0 residue 219 GLN 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 175 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 39 optimal weight: 0.0770 chunk 172 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 265 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 287 optimal weight: 7.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 N 219 GLN B 179 GLN D 195 ASN D 219 GLN ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN P 112 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 GLN 0 219 GLN 2 319 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.057789 restraints weight = 83474.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059479 restraints weight = 50363.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.060583 restraints weight = 37082.510| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 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 = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22690 Z= 0.115 Angle : 0.545 9.987 31140 Z= 0.272 Chirality : 0.038 0.187 3730 Planarity : 0.005 0.053 3980 Dihedral : 4.918 54.797 3187 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.95 % Allowed : 16.16 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.15), residues: 2985 helix: 1.76 (0.11), residues: 2100 sheet: None (None), residues: 0 loop : 1.12 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 23 HIS 0.003 0.001 HIS I 84 PHE 0.010 0.001 PHE L 40 TYR 0.020 0.001 TYR Q 164 ARG 0.010 0.001 ARG H 82 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 1420) hydrogen bonds : angle 3.92256 ( 4185) covalent geometry : bond 0.00254 (22690) covalent geometry : angle 0.54486 (31140) *********************** 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 531 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 468 time to evaluate : 5.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8873 (m-30) cc_final: 0.8272 (m-30) REVERT: L 143 ARG cc_start: 0.9135 (tpt90) cc_final: 0.8378 (tpm170) REVERT: L 144 MET cc_start: 0.8699 (ttm) cc_final: 0.8263 (ttm) REVERT: L 214 MET cc_start: 0.8938 (mtm) cc_final: 0.8573 (mtp) REVERT: M 35 GLU cc_start: 0.8715 (pt0) cc_final: 0.8240 (tt0) REVERT: M 76 GLU cc_start: 0.8675 (tp30) cc_final: 0.8411 (tp30) REVERT: N 164 TYR cc_start: 0.8939 (t80) cc_final: 0.8310 (t80) REVERT: N 192 GLN cc_start: 0.8907 (tp40) cc_final: 0.8560 (tp-100) REVERT: N 215 MET cc_start: 0.8965 (ttm) cc_final: 0.8573 (ttp) REVERT: B 51 ASP cc_start: 0.8875 (m-30) cc_final: 0.8261 (m-30) REVERT: C 32 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: C 35 GLU cc_start: 0.8748 (pt0) cc_final: 0.7976 (tt0) REVERT: C 76 GLU cc_start: 0.8692 (tp30) cc_final: 0.8255 (tp30) REVERT: C 114 GLN cc_start: 0.9318 (mt0) cc_final: 0.8737 (mp10) REVERT: D 164 TYR cc_start: 0.8887 (t80) cc_final: 0.8081 (t80) REVERT: D 171 THR cc_start: 0.9131 (m) cc_final: 0.8856 (p) REVERT: D 192 GLN cc_start: 0.8941 (tp40) cc_final: 0.8629 (tp-100) REVERT: G 57 ASN cc_start: 0.9042 (m-40) cc_final: 0.8440 (t0) REVERT: H 51 ASP cc_start: 0.9048 (m-30) cc_final: 0.8384 (m-30) REVERT: H 176 GLN cc_start: 0.8375 (mt0) cc_final: 0.8170 (mt0) REVERT: I 76 GLU cc_start: 0.8700 (tp30) cc_final: 0.8228 (tp30) REVERT: I 114 GLN cc_start: 0.9366 (mt0) cc_final: 0.8906 (mp10) REVERT: J 164 TYR cc_start: 0.8854 (t80) cc_final: 0.8424 (t80) REVERT: P 66 MET cc_start: 0.8972 (tpt) cc_final: 0.8659 (tpt) REVERT: P 109 SER cc_start: 0.7077 (OUTLIER) cc_final: 0.6693 (m) REVERT: Q 51 ASP cc_start: 0.8905 (m-30) cc_final: 0.8429 (m-30) REVERT: R 35 GLU cc_start: 0.8785 (pt0) cc_final: 0.8024 (tp30) REVERT: R 41 SER cc_start: 0.9164 (t) cc_final: 0.8951 (p) REVERT: R 76 GLU cc_start: 0.8707 (tp30) cc_final: 0.8390 (tp30) REVERT: R 114 GLN cc_start: 0.9332 (mt0) cc_final: 0.8751 (mp10) REVERT: S 164 TYR cc_start: 0.8921 (t80) cc_final: 0.8357 (t80) REVERT: U 317 PRO cc_start: 0.9535 (Cg_exo) cc_final: 0.9307 (Cg_endo) REVERT: V 57 ASN cc_start: 0.9062 (m-40) cc_final: 0.8410 (t0) REVERT: V 109 SER cc_start: 0.7341 (OUTLIER) cc_final: 0.6974 (m) REVERT: W 51 ASP cc_start: 0.8955 (m-30) cc_final: 0.8435 (m-30) REVERT: W 67 GLN cc_start: 0.8565 (tp40) cc_final: 0.8258 (tp40) REVERT: W 179 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8072 (mm-40) REVERT: W 185 MET cc_start: 0.8782 (mtm) cc_final: 0.8210 (mtp) REVERT: X 35 GLU cc_start: 0.8660 (pt0) cc_final: 0.7990 (tt0) REVERT: X 68 MET cc_start: 0.9315 (mtp) cc_final: 0.8971 (mtt) REVERT: X 114 GLN cc_start: 0.9352 (mt0) cc_final: 0.8777 (mp10) REVERT: 0 164 TYR cc_start: 0.8909 (t80) cc_final: 0.8398 (t80) REVERT: 3 185 MET cc_start: 0.9163 (mtm) cc_final: 0.8941 (mtm) outliers start: 63 outliers final: 34 residues processed: 515 average time/residue: 0.5334 time to fit residues: 446.8175 Evaluate side-chains 463 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 425 time to evaluate : 4.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 32 PHE 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 A residue 16 SER Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 VAL 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 D residue 219 GLN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain H residue 37 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 Q residue 37 ILE 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 59 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 179 GLN Chi-restraints excluded: chain X residue 32 PHE 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 35 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 181 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 148 optimal weight: 0.0970 chunk 241 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 32 optimal weight: 0.0270 chunk 194 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 overall best weight: 0.8238 ------------------------------------------------------------------------------- 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** 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** ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 195 ASN 2 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058319 restraints weight = 83229.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059992 restraints weight = 50331.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.061078 restraints weight = 37140.894| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 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 = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22690 Z= 0.111 Angle : 0.561 10.931 31140 Z= 0.274 Chirality : 0.038 0.201 3730 Planarity : 0.005 0.053 3980 Dihedral : 4.635 54.183 3171 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.48 % Allowed : 17.66 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.15), residues: 2985 helix: 1.80 (0.11), residues: 2100 sheet: None (None), residues: 0 loop : 1.09 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 3 117 HIS 0.003 0.000 HIS I 84 PHE 0.010 0.001 PHE Z 321 TYR 0.023 0.001 TYR L 164 ARG 0.008 0.000 ARG H 143 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 1420) hydrogen bonds : angle 3.82307 ( 4185) covalent geometry : bond 0.00250 (22690) covalent geometry : angle 0.56116 (31140) *********************** 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 513 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 460 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9548 (ttmm) cc_final: 0.9336 (tppp) REVERT: L 51 ASP cc_start: 0.8883 (m-30) cc_final: 0.8303 (m-30) REVERT: L 55 MET cc_start: 0.9051 (tmm) cc_final: 0.8808 (tmm) REVERT: L 144 MET cc_start: 0.8567 (ttm) cc_final: 0.8266 (ttm) REVERT: M 35 GLU cc_start: 0.8820 (pt0) cc_final: 0.8139 (tt0) REVERT: M 76 GLU cc_start: 0.8716 (tp30) cc_final: 0.8417 (tp30) REVERT: N 164 TYR cc_start: 0.8932 (t80) cc_final: 0.8323 (t80) REVERT: N 192 GLN cc_start: 0.8941 (tp40) cc_final: 0.8595 (tp-100) REVERT: N 215 MET cc_start: 0.8976 (ttm) cc_final: 0.8583 (ttp) REVERT: A 57 ASN cc_start: 0.9044 (m-40) cc_final: 0.8426 (t0) REVERT: B 51 ASP cc_start: 0.8874 (m-30) cc_final: 0.8243 (m-30) REVERT: C 32 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: C 35 GLU cc_start: 0.8729 (pt0) cc_final: 0.7975 (tt0) REVERT: C 76 GLU cc_start: 0.8724 (tp30) cc_final: 0.8366 (tp30) REVERT: C 114 GLN cc_start: 0.9359 (mt0) cc_final: 0.8867 (mp10) REVERT: D 164 TYR cc_start: 0.8895 (t80) cc_final: 0.8127 (t80) REVERT: G 55 MET cc_start: 0.9043 (mtp) cc_final: 0.8711 (mtp) REVERT: G 57 ASN cc_start: 0.9025 (m-40) cc_final: 0.8471 (t0) REVERT: H 51 ASP cc_start: 0.9053 (m-30) cc_final: 0.8405 (m-30) REVERT: H 66 MET cc_start: 0.8327 (mmm) cc_final: 0.7994 (mmm) REVERT: H 164 TYR cc_start: 0.8785 (t80) cc_final: 0.8347 (t80) REVERT: H 176 GLN cc_start: 0.8351 (mt0) cc_final: 0.8040 (mt0) REVERT: I 76 GLU cc_start: 0.8714 (tp30) cc_final: 0.8272 (tp30) REVERT: I 114 GLN cc_start: 0.9377 (mt0) cc_final: 0.8945 (mp10) REVERT: J 164 TYR cc_start: 0.8866 (t80) cc_final: 0.8450 (t80) REVERT: P 109 SER cc_start: 0.7082 (OUTLIER) cc_final: 0.6715 (m) REVERT: P 215 MET cc_start: 0.8632 (mtt) cc_final: 0.8339 (mtm) REVERT: Q 51 ASP cc_start: 0.8932 (m-30) cc_final: 0.8476 (m-30) REVERT: R 35 GLU cc_start: 0.8818 (pt0) cc_final: 0.7984 (tp30) REVERT: R 41 SER cc_start: 0.9180 (t) cc_final: 0.8959 (p) REVERT: R 76 GLU cc_start: 0.8787 (tp30) cc_final: 0.8364 (tp30) REVERT: R 114 GLN cc_start: 0.9374 (mt0) cc_final: 0.8925 (mp10) REVERT: S 164 TYR cc_start: 0.8918 (t80) cc_final: 0.8355 (t80) REVERT: U 317 PRO cc_start: 0.9558 (Cg_exo) cc_final: 0.9338 (Cg_endo) REVERT: V 57 ASN cc_start: 0.9061 (m-40) cc_final: 0.8431 (t0) REVERT: W 51 ASP cc_start: 0.8972 (m-30) cc_final: 0.8423 (m-30) REVERT: W 67 GLN cc_start: 0.8552 (tp40) cc_final: 0.8266 (tp40) REVERT: W 185 MET cc_start: 0.8818 (mtm) cc_final: 0.8270 (mtp) REVERT: X 35 GLU cc_start: 0.8702 (pt0) cc_final: 0.7983 (tt0) REVERT: X 114 GLN cc_start: 0.9367 (mt0) cc_final: 0.8779 (mp10) REVERT: 0 164 TYR cc_start: 0.8942 (t80) cc_final: 0.8413 (t80) REVERT: 0 202 LEU cc_start: 0.8990 (tp) cc_final: 0.8756 (tp) outliers start: 53 outliers final: 35 residues processed: 500 average time/residue: 0.3149 time to fit residues: 254.5649 Evaluate side-chains 464 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 427 time to evaluate : 2.836 ------------------------------------------------------------------------------- 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 A residue 16 SER Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 VAL 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 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 195 ASN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 109 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 69 LEU 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 59 VAL 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 1 residue 315 LEU Chi-restraints excluded: chain 3 residue 16 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 21 optimal weight: 7.9990 chunk 149 optimal weight: 0.1980 chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 113 optimal weight: 0.0770 chunk 174 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 219 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN W 179 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.078002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.059102 restraints weight = 82889.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.060800 restraints weight = 50070.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061902 restraints weight = 36900.489| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22690 Z= 0.110 Angle : 0.564 10.666 31140 Z= 0.275 Chirality : 0.038 0.203 3730 Planarity : 0.005 0.053 3980 Dihedral : 4.508 53.534 3169 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.62 % Allowed : 18.03 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.15), residues: 2985 helix: 1.77 (0.11), residues: 2105 sheet: None (None), residues: 0 loop : 1.13 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 3 23 HIS 0.004 0.001 HIS I 84 PHE 0.010 0.001 PHE L 40 TYR 0.029 0.001 TYR L 164 ARG 0.013 0.001 ARG H 82 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 1420) hydrogen bonds : angle 3.78130 ( 4185) covalent geometry : bond 0.00246 (22690) covalent geometry : angle 0.56355 (31140) *********************** 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: 56 poor density : 469 time to evaluate : 6.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9556 (ttmm) cc_final: 0.9338 (tppp) REVERT: L 51 ASP cc_start: 0.8910 (m-30) cc_final: 0.8345 (m-30) REVERT: L 143 ARG cc_start: 0.9183 (tpt90) cc_final: 0.8853 (tpm170) REVERT: L 144 MET cc_start: 0.8519 (ttm) cc_final: 0.8169 (ttm) REVERT: L 179 GLN cc_start: 0.7508 (tp40) cc_final: 0.7186 (tp40) REVERT: M 35 GLU cc_start: 0.8858 (pt0) cc_final: 0.8190 (tt0) REVERT: M 76 GLU cc_start: 0.8735 (tp30) cc_final: 0.8417 (tp30) REVERT: N 164 TYR cc_start: 0.8916 (t80) cc_final: 0.8297 (t80) REVERT: N 192 GLN cc_start: 0.8966 (tp40) cc_final: 0.8613 (tp-100) REVERT: N 205 LEU cc_start: 0.8844 (tp) cc_final: 0.8588 (tt) REVERT: N 215 MET cc_start: 0.8989 (ttm) cc_final: 0.8627 (ttp) REVERT: A 57 ASN cc_start: 0.9026 (m-40) cc_final: 0.8448 (t0) REVERT: A 195 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8454 (p0) REVERT: B 51 ASP cc_start: 0.8906 (m-30) cc_final: 0.8318 (m-30) REVERT: B 55 MET cc_start: 0.9022 (tmm) cc_final: 0.8718 (tmm) REVERT: C 32 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: C 35 GLU cc_start: 0.8734 (pt0) cc_final: 0.7979 (tt0) REVERT: C 76 GLU cc_start: 0.8775 (tp30) cc_final: 0.8403 (tp30) REVERT: C 102 SER cc_start: 0.8783 (t) cc_final: 0.8357 (t) REVERT: C 114 GLN cc_start: 0.9354 (mt0) cc_final: 0.8927 (mp10) REVERT: D 164 TYR cc_start: 0.8938 (t80) cc_final: 0.8071 (t80) REVERT: F 316 PHE cc_start: 0.8424 (m-80) cc_final: 0.7717 (m-80) REVERT: G 55 MET cc_start: 0.9027 (mtp) cc_final: 0.8669 (mtp) REVERT: G 57 ASN cc_start: 0.9012 (m-40) cc_final: 0.8450 (t0) REVERT: G 195 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8421 (p0) REVERT: H 25 LYS cc_start: 0.9515 (ttmm) cc_final: 0.9305 (tppp) REVERT: H 51 ASP cc_start: 0.9088 (m-30) cc_final: 0.8437 (m-30) REVERT: H 55 MET cc_start: 0.9076 (tmm) cc_final: 0.8808 (tmm) REVERT: H 66 MET cc_start: 0.8320 (mmm) cc_final: 0.8038 (mmm) REVERT: H 143 ARG cc_start: 0.9156 (tpt90) cc_final: 0.8672 (tpm170) REVERT: H 164 TYR cc_start: 0.8766 (t80) cc_final: 0.8448 (t80) REVERT: H 176 GLN cc_start: 0.8298 (mt0) cc_final: 0.8076 (mt0) REVERT: I 76 GLU cc_start: 0.8706 (tp30) cc_final: 0.8288 (tp30) REVERT: I 102 SER cc_start: 0.8758 (t) cc_final: 0.8317 (t) REVERT: I 114 GLN cc_start: 0.9407 (mt0) cc_final: 0.8995 (mp10) REVERT: J 164 TYR cc_start: 0.8879 (t80) cc_final: 0.8594 (t80) REVERT: Q 51 ASP cc_start: 0.8965 (m-30) cc_final: 0.8515 (m-30) REVERT: R 35 GLU cc_start: 0.8850 (pt0) cc_final: 0.7981 (tp30) REVERT: R 41 SER cc_start: 0.9202 (t) cc_final: 0.8954 (p) REVERT: R 76 GLU cc_start: 0.8824 (tp30) cc_final: 0.8347 (tp30) REVERT: R 114 GLN cc_start: 0.9327 (mt0) cc_final: 0.9012 (mp10) REVERT: S 164 TYR cc_start: 0.8939 (t80) cc_final: 0.8340 (t80) REVERT: U 317 PRO cc_start: 0.9554 (Cg_exo) cc_final: 0.9294 (Cg_endo) REVERT: V 57 ASN cc_start: 0.9012 (m-40) cc_final: 0.8413 (t0) REVERT: W 51 ASP cc_start: 0.9012 (m-30) cc_final: 0.8452 (m-30) REVERT: W 55 MET cc_start: 0.9051 (tmm) cc_final: 0.8796 (tmm) REVERT: W 66 MET cc_start: 0.8436 (mmm) cc_final: 0.8186 (mmm) REVERT: W 67 GLN cc_start: 0.8624 (tp40) cc_final: 0.8377 (tp40) REVERT: W 185 MET cc_start: 0.8856 (mtm) cc_final: 0.8294 (mtp) REVERT: X 35 GLU cc_start: 0.8673 (pt0) cc_final: 0.7949 (tt0) REVERT: X 114 GLN cc_start: 0.9369 (mt0) cc_final: 0.8878 (mp10) REVERT: 0 164 TYR cc_start: 0.8961 (t80) cc_final: 0.8428 (t80) REVERT: 0 202 LEU cc_start: 0.9042 (tp) cc_final: 0.8757 (tp) REVERT: 3 66 MET cc_start: 0.8884 (tpt) cc_final: 0.8422 (tpt) outliers start: 56 outliers final: 42 residues processed: 514 average time/residue: 0.3432 time to fit residues: 288.5938 Evaluate side-chains 475 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 430 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR 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 A residue 16 SER Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 149 SER 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 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 O residue 319 GLN Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 69 LEU 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 111 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 179 GLN 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 1 residue 315 LEU Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 174 optimal weight: 0.4980 chunk 279 optimal weight: 0.0020 chunk 78 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 240 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 70 optimal weight: 0.0170 chunk 29 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 254 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 overall best weight: 0.2826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN F 319 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 179 GLN 2 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060021 restraints weight = 82966.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.061740 restraints weight = 50096.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.062850 restraints weight = 36864.031| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22690 Z= 0.114 Angle : 0.596 11.578 31140 Z= 0.286 Chirality : 0.038 0.208 3730 Planarity : 0.005 0.054 3980 Dihedral : 4.420 53.064 3167 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.25 % Allowed : 19.16 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.15), residues: 2985 helix: 1.80 (0.11), residues: 2095 sheet: None (None), residues: 0 loop : 1.23 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 23 HIS 0.002 0.000 HIS P 62 PHE 0.015 0.001 PHE B 40 TYR 0.031 0.001 TYR Q 164 ARG 0.008 0.001 ARG M 82 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 1420) hydrogen bonds : angle 3.74223 ( 4185) covalent geometry : bond 0.00257 (22690) covalent geometry : angle 0.59593 (31140) *********************** 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 524 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 476 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9549 (ttmm) cc_final: 0.9309 (tppp) REVERT: L 51 ASP cc_start: 0.8919 (m-30) cc_final: 0.8366 (m-30) REVERT: L 143 ARG cc_start: 0.9168 (tpt90) cc_final: 0.8838 (tpm170) REVERT: L 144 MET cc_start: 0.8530 (ttm) cc_final: 0.8066 (ttm) REVERT: L 179 GLN cc_start: 0.7886 (tp40) cc_final: 0.7646 (tp40) REVERT: M 35 GLU cc_start: 0.8831 (pt0) cc_final: 0.8206 (tt0) REVERT: M 76 GLU cc_start: 0.8750 (tp30) cc_final: 0.8462 (tp30) REVERT: M 102 SER cc_start: 0.8791 (t) cc_final: 0.8392 (t) REVERT: N 164 TYR cc_start: 0.8935 (t80) cc_final: 0.8309 (t80) REVERT: N 192 GLN cc_start: 0.8887 (tp40) cc_final: 0.8505 (tp-100) REVERT: N 215 MET cc_start: 0.8964 (ttm) cc_final: 0.8498 (ttp) REVERT: A 57 ASN cc_start: 0.8968 (m-40) cc_final: 0.8437 (t0) REVERT: B 51 ASP cc_start: 0.8908 (m-30) cc_final: 0.8321 (m-30) REVERT: C 35 GLU cc_start: 0.8723 (pt0) cc_final: 0.7979 (tt0) REVERT: C 66 MET cc_start: 0.8462 (mmm) cc_final: 0.8025 (mmm) REVERT: C 76 GLU cc_start: 0.8727 (tp30) cc_final: 0.8366 (tp30) REVERT: C 102 SER cc_start: 0.8729 (t) cc_final: 0.8299 (t) REVERT: C 114 GLN cc_start: 0.9303 (mt0) cc_final: 0.8991 (mp10) REVERT: F 316 PHE cc_start: 0.8391 (m-80) cc_final: 0.7813 (m-80) REVERT: G 57 ASN cc_start: 0.9010 (m-40) cc_final: 0.8471 (t0) REVERT: G 185 MET cc_start: 0.8708 (mtp) cc_final: 0.8413 (mtp) REVERT: H 25 LYS cc_start: 0.9495 (ttmm) cc_final: 0.9290 (tppp) REVERT: H 51 ASP cc_start: 0.9090 (m-30) cc_final: 0.8436 (m-30) REVERT: H 66 MET cc_start: 0.8305 (mmm) cc_final: 0.8042 (mmm) REVERT: H 143 ARG cc_start: 0.9105 (tpt90) cc_final: 0.8656 (tpm170) REVERT: H 164 TYR cc_start: 0.8775 (t80) cc_final: 0.8485 (t80) REVERT: I 35 GLU cc_start: 0.8500 (pt0) cc_final: 0.7899 (tp30) REVERT: I 76 GLU cc_start: 0.8734 (tp30) cc_final: 0.8350 (tp30) REVERT: I 102 SER cc_start: 0.8772 (t) cc_final: 0.8352 (t) REVERT: I 114 GLN cc_start: 0.9393 (mt0) cc_final: 0.9009 (mp10) REVERT: J 164 TYR cc_start: 0.8827 (t80) cc_final: 0.8547 (t80) REVERT: P 215 MET cc_start: 0.8702 (mtt) cc_final: 0.8433 (mtt) REVERT: Q 51 ASP cc_start: 0.8977 (m-30) cc_final: 0.8500 (m-30) REVERT: Q 143 ARG cc_start: 0.9284 (tpt90) cc_final: 0.8816 (tpm170) REVERT: R 35 GLU cc_start: 0.8815 (pt0) cc_final: 0.7975 (tp30) REVERT: R 41 SER cc_start: 0.9201 (t) cc_final: 0.8948 (p) REVERT: R 76 GLU cc_start: 0.8814 (tp30) cc_final: 0.8304 (tp30) REVERT: S 164 TYR cc_start: 0.8912 (t80) cc_final: 0.8394 (t80) REVERT: S 215 MET cc_start: 0.8949 (ttm) cc_final: 0.8411 (ttp) REVERT: U 317 PRO cc_start: 0.9522 (Cg_exo) cc_final: 0.9283 (Cg_endo) REVERT: V 57 ASN cc_start: 0.9004 (m-40) cc_final: 0.8411 (t0) REVERT: W 51 ASP cc_start: 0.8980 (m-30) cc_final: 0.8425 (m-30) REVERT: W 55 MET cc_start: 0.9095 (tmm) cc_final: 0.8823 (tmm) REVERT: W 67 GLN cc_start: 0.8695 (tp40) cc_final: 0.8446 (tp40) REVERT: W 185 MET cc_start: 0.8850 (mtm) cc_final: 0.8294 (mtp) REVERT: X 35 GLU cc_start: 0.8465 (pt0) cc_final: 0.7896 (tt0) REVERT: 0 164 TYR cc_start: 0.8949 (t80) cc_final: 0.8427 (t80) REVERT: 0 202 LEU cc_start: 0.9060 (tp) cc_final: 0.8773 (tp) REVERT: 3 13 GLN cc_start: 0.8811 (tp40) cc_final: 0.8575 (tp40) REVERT: 3 66 MET cc_start: 0.8915 (tpt) cc_final: 0.8466 (tpt) outliers start: 48 outliers final: 38 residues processed: 513 average time/residue: 0.3339 time to fit residues: 276.1434 Evaluate side-chains 481 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 443 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR 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 A residue 35 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 35 GLU 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 O residue 319 GLN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN 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 V residue 111 LEU 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 1 residue 315 LEU Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 95 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 10 optimal weight: 40.0000 chunk 178 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 chunk 251 optimal weight: 0.9980 chunk 281 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 F 319 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 63 GLN S 179 GLN S 193 ASN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 319 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.075275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.055981 restraints weight = 84670.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057625 restraints weight = 51457.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.058708 restraints weight = 38073.890| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 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 = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 22690 Z= 0.200 Angle : 0.658 13.435 31140 Z= 0.326 Chirality : 0.041 0.208 3730 Planarity : 0.005 0.057 3980 Dihedral : 4.536 54.816 3165 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.30 % Allowed : 19.91 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.15), residues: 2985 helix: 1.75 (0.11), residues: 2095 sheet: None (None), residues: 0 loop : 1.17 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 80 HIS 0.003 0.001 HIS A 12 PHE 0.016 0.002 PHE Z 321 TYR 0.038 0.002 TYR Q 164 ARG 0.018 0.001 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 1420) hydrogen bonds : angle 4.12838 ( 4185) covalent geometry : bond 0.00473 (22690) covalent geometry : angle 0.65817 (31140) *********************** 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 473 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 424 time to evaluate : 3.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9557 (ttmm) cc_final: 0.9332 (tppp) REVERT: L 51 ASP cc_start: 0.8931 (m-30) cc_final: 0.8356 (m-30) REVERT: L 144 MET cc_start: 0.8569 (ttm) cc_final: 0.8047 (ttm) REVERT: L 164 TYR cc_start: 0.8470 (t80) cc_final: 0.8155 (t80) REVERT: M 35 GLU cc_start: 0.8812 (pt0) cc_final: 0.8288 (tt0) REVERT: M 76 GLU cc_start: 0.8796 (tp30) cc_final: 0.8545 (tp30) REVERT: N 164 TYR cc_start: 0.9020 (t80) cc_final: 0.8287 (t80) REVERT: N 192 GLN cc_start: 0.8934 (tp40) cc_final: 0.8536 (tp-100) REVERT: N 215 MET cc_start: 0.9001 (ttm) cc_final: 0.8511 (ttp) REVERT: A 195 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8465 (p0) REVERT: C 35 GLU cc_start: 0.8784 (pt0) cc_final: 0.8061 (tt0) REVERT: C 76 GLU cc_start: 0.8780 (tp30) cc_final: 0.8382 (tp30) REVERT: C 114 GLN cc_start: 0.9379 (mt0) cc_final: 0.9032 (mp10) REVERT: G 44 SER cc_start: 0.8980 (m) cc_final: 0.8388 (p) REVERT: H 25 LYS cc_start: 0.9530 (ttmm) cc_final: 0.9316 (tppp) REVERT: H 44 SER cc_start: 0.9053 (p) cc_final: 0.8803 (p) REVERT: H 51 ASP cc_start: 0.9062 (m-30) cc_final: 0.8425 (m-30) REVERT: I 76 GLU cc_start: 0.8724 (tp30) cc_final: 0.8333 (tp30) REVERT: I 114 GLN cc_start: 0.9388 (mt0) cc_final: 0.9024 (mp10) REVERT: J 164 TYR cc_start: 0.8885 (t80) cc_final: 0.8474 (t80) REVERT: P 44 SER cc_start: 0.8919 (m) cc_final: 0.8221 (p) REVERT: Q 25 LYS cc_start: 0.9604 (ttmm) cc_final: 0.9376 (tppp) REVERT: Q 51 ASP cc_start: 0.8978 (m-30) cc_final: 0.8505 (m-30) REVERT: Q 55 MET cc_start: 0.9282 (ttp) cc_final: 0.8991 (tmm) REVERT: R 35 GLU cc_start: 0.8885 (pt0) cc_final: 0.8076 (tp30) REVERT: R 76 GLU cc_start: 0.8844 (tp30) cc_final: 0.8370 (tp30) REVERT: S 164 TYR cc_start: 0.9017 (t80) cc_final: 0.8396 (t80) REVERT: V 44 SER cc_start: 0.8983 (m) cc_final: 0.8632 (p) REVERT: W 51 ASP cc_start: 0.9017 (m-30) cc_final: 0.8438 (m-30) REVERT: W 176 GLN cc_start: 0.8357 (mt0) cc_final: 0.8140 (mt0) REVERT: X 35 GLU cc_start: 0.8699 (pt0) cc_final: 0.7988 (tt0) REVERT: 0 164 TYR cc_start: 0.9048 (t80) cc_final: 0.8477 (t80) REVERT: 0 193 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7422 (t0) REVERT: 3 44 SER cc_start: 0.8977 (m) cc_final: 0.8269 (p) outliers start: 49 outliers final: 35 residues processed: 464 average time/residue: 0.4242 time to fit residues: 319.3116 Evaluate side-chains 450 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 413 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR 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 A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 179 GLN 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 35 GLU Chi-restraints excluded: chain I residue 15 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 J residue 195 ASN Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain S residue 178 SER 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 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 193 ASN Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 1 residue 315 LEU Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 36 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 255 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 260 optimal weight: 6.9990 chunk 204 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 114 GLN B 179 GLN F 319 GLN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.076406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057188 restraints weight = 83861.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.058869 restraints weight = 50588.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059946 restraints weight = 37298.413| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 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 = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22690 Z= 0.136 Angle : 0.638 13.576 31140 Z= 0.309 Chirality : 0.040 0.228 3730 Planarity : 0.005 0.058 3980 Dihedral : 4.507 57.086 3163 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.25 % Allowed : 20.37 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.16), residues: 2985 helix: 1.76 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : 1.16 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 184 HIS 0.002 0.000 HIS H 62 PHE 0.015 0.001 PHE Z 321 TYR 0.037 0.001 TYR Q 164 ARG 0.013 0.001 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 1420) hydrogen bonds : angle 3.97448 ( 4185) covalent geometry : bond 0.00331 (22690) covalent geometry : angle 0.63847 (31140) *********************** 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 488 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 440 time to evaluate : 4.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9551 (ttmm) cc_final: 0.9326 (tppp) REVERT: L 51 ASP cc_start: 0.8908 (m-30) cc_final: 0.8335 (m-30) REVERT: L 55 MET cc_start: 0.9002 (tmm) cc_final: 0.8751 (tmm) REVERT: L 143 ARG cc_start: 0.9203 (tpt90) cc_final: 0.8815 (tpm170) REVERT: L 144 MET cc_start: 0.8626 (ttm) cc_final: 0.8197 (ttm) REVERT: L 164 TYR cc_start: 0.8483 (t80) cc_final: 0.8193 (t80) REVERT: M 35 GLU cc_start: 0.8824 (pt0) cc_final: 0.8228 (tt0) REVERT: M 76 GLU cc_start: 0.8794 (tp30) cc_final: 0.8547 (tp30) REVERT: M 102 SER cc_start: 0.8764 (t) cc_final: 0.8295 (t) REVERT: N 164 TYR cc_start: 0.8984 (t80) cc_final: 0.8276 (t80) REVERT: N 192 GLN cc_start: 0.8877 (tp40) cc_final: 0.8612 (tp-100) REVERT: N 215 MET cc_start: 0.9047 (ttm) cc_final: 0.8596 (ttp) REVERT: A 57 ASN cc_start: 0.9101 (m-40) cc_final: 0.8456 (t0) REVERT: A 195 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8400 (p0) REVERT: B 55 MET cc_start: 0.8891 (tmm) cc_final: 0.8436 (tmm) REVERT: C 35 GLU cc_start: 0.8734 (pt0) cc_final: 0.8004 (tt0) REVERT: C 76 GLU cc_start: 0.8762 (tp30) cc_final: 0.8379 (tp30) REVERT: C 114 GLN cc_start: 0.9351 (mt0) cc_final: 0.9026 (mp10) REVERT: G 44 SER cc_start: 0.8855 (m) cc_final: 0.8168 (p) REVERT: G 57 ASN cc_start: 0.9014 (m-40) cc_final: 0.8474 (t0) REVERT: G 185 MET cc_start: 0.8703 (mtp) cc_final: 0.8232 (mtp) REVERT: H 25 LYS cc_start: 0.9516 (ttmm) cc_final: 0.9295 (tppp) REVERT: H 44 SER cc_start: 0.9024 (p) cc_final: 0.8757 (p) REVERT: H 51 ASP cc_start: 0.9057 (m-30) cc_final: 0.8421 (m-30) REVERT: H 55 MET cc_start: 0.9004 (tmm) cc_final: 0.8752 (tmm) REVERT: H 143 ARG cc_start: 0.9241 (tpt90) cc_final: 0.8838 (tpm170) REVERT: I 35 GLU cc_start: 0.8508 (pt0) cc_final: 0.7907 (tp30) REVERT: I 76 GLU cc_start: 0.8715 (tp30) cc_final: 0.8326 (tp30) REVERT: I 102 SER cc_start: 0.8796 (t) cc_final: 0.8353 (t) REVERT: J 164 TYR cc_start: 0.8926 (t80) cc_final: 0.8517 (t80) REVERT: P 44 SER cc_start: 0.8805 (m) cc_final: 0.8019 (p) REVERT: Q 25 LYS cc_start: 0.9597 (ttmm) cc_final: 0.9382 (tppp) REVERT: Q 51 ASP cc_start: 0.8940 (m-30) cc_final: 0.8489 (m-30) REVERT: Q 55 MET cc_start: 0.9219 (ttp) cc_final: 0.9011 (tmm) REVERT: Q 143 ARG cc_start: 0.9323 (tpt90) cc_final: 0.8927 (tpm170) REVERT: R 35 GLU cc_start: 0.8833 (pt0) cc_final: 0.8029 (tp30) REVERT: R 76 GLU cc_start: 0.8822 (tp30) cc_final: 0.8361 (tp30) REVERT: R 114 GLN cc_start: 0.9345 (mt0) cc_final: 0.9023 (mp10) REVERT: R 134 ILE cc_start: 0.9060 (mm) cc_final: 0.8860 (mm) REVERT: S 164 TYR cc_start: 0.9007 (t80) cc_final: 0.8336 (t80) REVERT: S 215 MET cc_start: 0.8863 (ttm) cc_final: 0.8625 (ttp) REVERT: V 44 SER cc_start: 0.8846 (m) cc_final: 0.8446 (p) REVERT: V 57 ASN cc_start: 0.9083 (m-40) cc_final: 0.8426 (t0) REVERT: W 51 ASP cc_start: 0.8982 (m-30) cc_final: 0.8419 (m-30) REVERT: W 55 MET cc_start: 0.9021 (tmm) cc_final: 0.8777 (tmm) REVERT: W 176 GLN cc_start: 0.8312 (mt0) cc_final: 0.7947 (mt0) REVERT: X 35 GLU cc_start: 0.8489 (pt0) cc_final: 0.7929 (tt0) REVERT: 0 164 TYR cc_start: 0.9035 (t80) cc_final: 0.8468 (t80) REVERT: 0 202 LEU cc_start: 0.9004 (tp) cc_final: 0.8792 (tp) REVERT: 3 44 SER cc_start: 0.8919 (m) cc_final: 0.8081 (p) REVERT: 3 66 MET cc_start: 0.8930 (tpt) cc_final: 0.8500 (tpt) outliers start: 48 outliers final: 36 residues processed: 480 average time/residue: 0.4074 time to fit residues: 317.9682 Evaluate side-chains 466 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 429 time to evaluate : 4.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 149 SER 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 27 VAL Chi-restraints excluded: chain G residue 35 GLU 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 P residue 27 VAL Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain S residue 178 SER 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 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 1 residue 315 LEU Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 49 optimal weight: 0.9980 chunk 99 optimal weight: 0.2980 chunk 95 optimal weight: 5.9990 chunk 42 optimal weight: 0.0770 chunk 161 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 173 optimal weight: 0.0970 chunk 7 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 overall best weight: 1.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 114 GLN F 319 GLN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.058166 restraints weight = 83759.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059822 restraints weight = 50984.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060890 restraints weight = 37843.396| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 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 = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22690 Z= 0.126 Angle : 0.639 13.803 31140 Z= 0.309 Chirality : 0.039 0.232 3730 Planarity : 0.005 0.059 3980 Dihedral : 4.456 57.669 3163 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.15 % Allowed : 20.47 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.16), residues: 2985 helix: 1.77 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : 1.18 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 184 HIS 0.002 0.000 HIS B 62 PHE 0.015 0.001 PHE Z 321 TYR 0.031 0.001 TYR Q 164 ARG 0.011 0.001 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 1420) hydrogen bonds : angle 3.91705 ( 4185) covalent geometry : bond 0.00302 (22690) covalent geometry : angle 0.63938 (31140) ********************** 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 492 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 446 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9522 (ttmm) cc_final: 0.9290 (tppp) REVERT: L 51 ASP cc_start: 0.8896 (m-30) cc_final: 0.8399 (m-30) REVERT: L 55 MET cc_start: 0.8940 (tmm) cc_final: 0.8671 (tmm) REVERT: L 143 ARG cc_start: 0.9162 (tpt90) cc_final: 0.8796 (tpm170) REVERT: L 144 MET cc_start: 0.8585 (ttm) cc_final: 0.8087 (ttm) REVERT: L 164 TYR cc_start: 0.8436 (t80) cc_final: 0.8146 (t80) REVERT: M 35 GLU cc_start: 0.8786 (pt0) cc_final: 0.8210 (tt0) REVERT: M 76 GLU cc_start: 0.8799 (tp30) cc_final: 0.8529 (tp30) REVERT: M 102 SER cc_start: 0.8738 (t) cc_final: 0.8309 (t) REVERT: N 164 TYR cc_start: 0.8920 (t80) cc_final: 0.8260 (t80) REVERT: N 215 MET cc_start: 0.9073 (ttm) cc_final: 0.8637 (ttp) REVERT: A 44 SER cc_start: 0.8812 (m) cc_final: 0.8098 (p) REVERT: A 57 ASN cc_start: 0.9059 (m-40) cc_final: 0.8439 (t0) REVERT: A 102 SER cc_start: 0.8900 (m) cc_final: 0.8600 (t) REVERT: A 195 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8369 (p0) REVERT: B 55 MET cc_start: 0.8856 (tmm) cc_final: 0.8412 (tmm) REVERT: B 67 GLN cc_start: 0.8503 (tp40) cc_final: 0.8079 (tp40) REVERT: C 35 GLU cc_start: 0.8690 (pt0) cc_final: 0.7986 (tt0) REVERT: C 76 GLU cc_start: 0.8752 (tp30) cc_final: 0.8386 (tp30) REVERT: C 102 SER cc_start: 0.8803 (t) cc_final: 0.8375 (t) REVERT: C 114 GLN cc_start: 0.9316 (mt0) cc_final: 0.9027 (mp10) REVERT: G 44 SER cc_start: 0.8763 (m) cc_final: 0.8061 (p) REVERT: G 57 ASN cc_start: 0.8988 (m-40) cc_final: 0.8470 (t0) REVERT: G 185 MET cc_start: 0.8677 (mtp) cc_final: 0.8337 (mtp) REVERT: H 25 LYS cc_start: 0.9491 (ttmm) cc_final: 0.9267 (tppp) REVERT: H 44 SER cc_start: 0.9006 (p) cc_final: 0.8721 (p) REVERT: H 51 ASP cc_start: 0.9047 (m-30) cc_final: 0.8421 (m-30) REVERT: H 55 MET cc_start: 0.8993 (tmm) cc_final: 0.8732 (tmm) REVERT: H 143 ARG cc_start: 0.9183 (tpt90) cc_final: 0.8787 (tpm170) REVERT: I 35 GLU cc_start: 0.8445 (pt0) cc_final: 0.7876 (tp30) REVERT: I 76 GLU cc_start: 0.8672 (tp30) cc_final: 0.8348 (tp30) REVERT: I 102 SER cc_start: 0.8766 (t) cc_final: 0.8318 (t) REVERT: I 114 GLN cc_start: 0.9386 (mt0) cc_final: 0.9029 (mp10) REVERT: J 164 TYR cc_start: 0.8902 (t80) cc_final: 0.8474 (t80) REVERT: Q 51 ASP cc_start: 0.8916 (m-30) cc_final: 0.8468 (m-30) REVERT: Q 143 ARG cc_start: 0.9286 (tpt90) cc_final: 0.8899 (tpm170) REVERT: R 35 GLU cc_start: 0.8778 (pt0) cc_final: 0.7972 (tp30) REVERT: R 76 GLU cc_start: 0.8791 (tp30) cc_final: 0.8387 (tp30) REVERT: R 114 GLN cc_start: 0.9357 (mt0) cc_final: 0.9096 (mp10) REVERT: R 134 ILE cc_start: 0.8899 (mm) cc_final: 0.8698 (mm) REVERT: S 164 TYR cc_start: 0.8977 (t80) cc_final: 0.8340 (t80) REVERT: S 215 MET cc_start: 0.8849 (ttm) cc_final: 0.8616 (ttp) REVERT: V 44 SER cc_start: 0.8702 (m) cc_final: 0.8267 (p) REVERT: V 57 ASN cc_start: 0.9050 (m-40) cc_final: 0.8385 (t0) REVERT: W 51 ASP cc_start: 0.8967 (m-30) cc_final: 0.8416 (m-30) REVERT: W 55 MET cc_start: 0.9002 (tmm) cc_final: 0.8754 (tmm) REVERT: W 176 GLN cc_start: 0.8220 (mt0) cc_final: 0.7877 (mt0) REVERT: X 35 GLU cc_start: 0.8443 (pt0) cc_final: 0.7939 (tt0) REVERT: 0 164 TYR cc_start: 0.9014 (t80) cc_final: 0.8476 (t80) REVERT: 0 193 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7399 (t0) REVERT: 0 202 LEU cc_start: 0.9017 (tp) cc_final: 0.8813 (tp) REVERT: 3 44 SER cc_start: 0.8726 (m) cc_final: 0.7733 (p) REVERT: 3 66 MET cc_start: 0.8912 (tpt) cc_final: 0.8488 (tpt) REVERT: 3 102 SER cc_start: 0.8869 (m) cc_final: 0.8667 (t) REVERT: 3 185 MET cc_start: 0.8964 (mtm) cc_final: 0.8635 (ttm) outliers start: 46 outliers final: 38 residues processed: 484 average time/residue: 0.3463 time to fit residues: 271.1897 Evaluate side-chains 472 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 432 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 149 SER 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 27 VAL Chi-restraints excluded: chain G residue 35 GLU 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 P residue 27 VAL Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain S residue 178 SER 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 W residue 58 THR Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 68 MET Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 193 ASN Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 1 residue 315 LEU Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 147 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 263 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 283 optimal weight: 1.9990 chunk 174 optimal weight: 0.0270 chunk 141 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 overall best weight: 1.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 114 GLN N 193 ASN F 319 GLN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 ASN Q 179 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 319 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.058461 restraints weight = 83731.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060123 restraints weight = 51150.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.061203 restraints weight = 38037.065| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 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 = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22690 Z= 0.122 Angle : 0.631 13.583 31140 Z= 0.305 Chirality : 0.039 0.226 3730 Planarity : 0.005 0.057 3980 Dihedral : 4.446 56.817 3163 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.11 % Allowed : 20.75 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.16), residues: 2985 helix: 1.80 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : 1.16 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 3 23 HIS 0.002 0.000 HIS H 62 PHE 0.015 0.001 PHE Z 321 TYR 0.028 0.001 TYR H 164 ARG 0.011 0.001 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 1420) hydrogen bonds : angle 3.87643 ( 4185) covalent geometry : bond 0.00295 (22690) covalent geometry : angle 0.63132 (31140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9604.50 seconds wall clock time: 175 minutes 23.89 seconds (10523.89 seconds total)