Starting phenix.real_space_refine on Wed May 21 20:15:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejl_28186/05_2025/8ejl_28186.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejl_28186/05_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_28186/05_2025/8ejl_28186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejl_28186/05_2025/8ejl_28186.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejl_28186/05_2025/8ejl_28186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejl_28186/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.92, per 1000 atoms: 0.36 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: 6.40 Conformation dependent library (CDL) restraints added in 2.9 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: 2.28 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: 5.97 Time building geometry restraints manager: 7.25 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: 0.18 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.140 Set scattering table: 0.240 Process input model: 42.990 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.610 ------------------------------------------------------------------------------- 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 : 2.766 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: 0.2972 time to fit residues: 275.0985 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 : 2.540 ------------------------------------------------------------------------------- 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 = 0.055593 restraints weight = 82924.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.057222 restraints weight = 50964.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058282 restraints weight = 37797.047| |-----------------------------------------------------------------------------| 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 : 2.603 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: 0.9170 (ttp) cc_final: 0.8902 (tmm) REVERT: L 117 TRP cc_start: 0.8552 (OUTLIER) cc_final: 0.8139 (m-90) REVERT: L 143 ARG cc_start: 0.9161 (tpt90) cc_final: 0.8333 (tpm170) REVERT: L 144 MET cc_start: 0.8818 (ttm) cc_final: 0.8328 (ttm) REVERT: L 176 GLN cc_start: 0.8017 (mt0) cc_final: 0.7746 (mt0) REVERT: L 214 MET cc_start: 0.9114 (mtm) cc_final: 0.8864 (mtp) REVERT: M 35 GLU cc_start: 0.8729 (pt0) cc_final: 0.8334 (tt0) REVERT: M 76 GLU cc_start: 0.8595 (tp30) cc_final: 0.8366 (tp30) REVERT: N 164 TYR cc_start: 0.8972 (t80) cc_final: 0.8355 (t80) REVERT: N 192 GLN cc_start: 0.8920 (tp40) cc_final: 0.8555 (tp-100) REVERT: A 45 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8495 (tm-30) REVERT: A 51 ASP cc_start: 0.9186 (m-30) cc_final: 0.8945 (m-30) REVERT: B 67 GLN cc_start: 0.8677 (tp40) cc_final: 0.8371 (tp40) REVERT: B 117 TRP cc_start: 0.8390 (OUTLIER) cc_final: 0.8062 (m-90) REVERT: C 32 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: C 35 GLU cc_start: 0.8892 (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: 0.8315 (tp30) REVERT: C 114 GLN cc_start: 0.9178 (mt0) cc_final: 0.8417 (mp-120) REVERT: D 164 TYR cc_start: 0.8900 (t80) cc_final: 0.8068 (t80) REVERT: D 171 THR cc_start: 0.9318 (m) cc_final: 0.9013 (p) REVERT: D 192 GLN cc_start: 0.8937 (tp40) cc_final: 0.8690 (tp-100) REVERT: G 29 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7966 (mt-10) REVERT: G 55 MET cc_start: 0.9089 (mtp) cc_final: 0.8771 (mtp) REVERT: G 109 SER cc_start: 0.7116 (OUTLIER) cc_final: 0.6893 (m) REVERT: G 185 MET cc_start: 0.9080 (mtt) cc_final: 0.8872 (mtm) REVERT: H 51 ASP cc_start: 0.9090 (m-30) cc_final: 0.8401 (m-30) REVERT: H 67 GLN cc_start: 0.8788 (tp40) cc_final: 0.8474 (tp40) REVERT: H 84 HIS cc_start: 0.8269 (m90) cc_final: 0.8003 (m90) REVERT: H 117 TRP cc_start: 0.8586 (OUTLIER) cc_final: 0.8362 (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: 0.8394 (mmm) REVERT: I 114 GLN cc_start: 0.9280 (mt0) cc_final: 0.8602 (mp10) REVERT: J 164 TYR cc_start: 0.8902 (t80) cc_final: 0.8534 (t80) REVERT: P 66 MET cc_start: 0.9067 (tpt) cc_final: 0.8828 (tpt) REVERT: P 109 SER cc_start: 0.7136 (OUTLIER) cc_final: 0.6852 (m) REVERT: P 195 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8911 (p0) REVERT: P 215 MET cc_start: 0.8818 (mtt) cc_final: 0.8548 (mtt) REVERT: Q 51 ASP cc_start: 0.8864 (m-30) cc_final: 0.8299 (m-30) REVERT: Q 67 GLN cc_start: 0.8792 (tp40) cc_final: 0.8495 (tp40) REVERT: Q 79 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8316 (mm-30) REVERT: Q 179 GLN cc_start: 0.7882 (tp40) cc_final: 0.7090 (tp40) REVERT: R 35 GLU cc_start: 0.8934 (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: 0.9342 (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: 0.9010 (mtp) cc_final: 0.8792 (mtt) REVERT: V 109 SER cc_start: 0.7394 (OUTLIER) cc_final: 0.7059 (m) REVERT: V 195 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8876 (p0) REVERT: V 215 MET cc_start: 0.8845 (mtt) cc_final: 0.8470 (mtt) REVERT: W 51 ASP cc_start: 0.8982 (m-30) cc_final: 0.8477 (m-30) REVERT: W 67 GLN cc_start: 0.8686 (tp40) cc_final: 0.8317 (tp40) REVERT: X 35 GLU cc_start: 0.8734 (pt0) cc_final: 0.8014 (tt0) REVERT: X 114 GLN cc_start: 0.9303 (mt0) cc_final: 0.8623 (mp10) REVERT: 0 164 TYR cc_start: 0.8939 (t80) cc_final: 0.8411 (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: 0.8104 (tm-30) cc_final: 0.7798 (tm-30) REVERT: 3 195 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8838 (p0) outliers start: 95 outliers final: 61 residues processed: 571 average time/residue: 0.3053 time to fit residues: 275.4876 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 : 2.575 ------------------------------------------------------------------------------- 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: 0.0870 chunk 141 optimal weight: 6.9990 chunk 222 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 overall best weight: 1.2766 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.076065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.056922 restraints weight = 81781.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.058562 restraints weight = 49895.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059626 restraints weight = 37003.107| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 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 = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22690 Z= 0.120 Angle : 0.553 8.832 31140 Z= 0.278 Chirality : 0.040 0.213 3730 Planarity : 0.005 0.051 3980 Dihedral : 5.431 56.669 3202 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.65 % Allowed : 15.27 % 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 0.004 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 0.04269 ( 1420) hydrogen bonds : angle 4.13529 ( 4185) covalent geometry : bond 0.00267 (22690) covalent geometry : angle 0.55336 (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 539 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 461 time to evaluate : 2.667 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: 0.8902 (m-30) cc_final: 0.8330 (m-30) REVERT: L 144 MET cc_start: 0.8787 (ttm) cc_final: 0.8559 (ttm) REVERT: L 214 MET cc_start: 0.9029 (mtm) cc_final: 0.8721 (mtp) REVERT: M 35 GLU cc_start: 0.8774 (pt0) cc_final: 0.8257 (tt0) REVERT: M 76 GLU cc_start: 0.8583 (tp30) cc_final: 0.8282 (tp30) REVERT: N 164 TYR cc_start: 0.8950 (t80) cc_final: 0.8357 (t80) REVERT: N 192 GLN cc_start: 0.8914 (tp40) cc_final: 0.8556 (tp-100) REVERT: A 215 MET cc_start: 0.8874 (mtp) cc_final: 0.8576 (mtt) REVERT: B 51 ASP cc_start: 0.8945 (m-30) cc_final: 0.8297 (m-30) REVERT: B 215 MET cc_start: 0.8760 (ttm) cc_final: 0.8540 (mtp) REVERT: C 32 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: C 35 GLU cc_start: 0.8768 (pt0) cc_final: 0.8145 (tt0) REVERT: C 76 GLU cc_start: 0.8691 (tp30) cc_final: 0.8293 (tp30) REVERT: C 114 GLN cc_start: 0.9247 (mt0) cc_final: 0.8617 (mp10) REVERT: D 164 TYR cc_start: 0.8880 (t80) cc_final: 0.8027 (t80) REVERT: D 171 THR cc_start: 0.9238 (m) cc_final: 0.8905 (p) REVERT: D 192 GLN cc_start: 0.8951 (tp40) cc_final: 0.8699 (tp-100) REVERT: G 55 MET cc_start: 0.9018 (mtp) cc_final: 0.8791 (mtp) REVERT: H 51 ASP cc_start: 0.9063 (m-30) cc_final: 0.8399 (m-30) REVERT: H 143 ARG cc_start: 0.9156 (tpt90) cc_final: 0.8924 (tpt90) REVERT: I 76 GLU cc_start: 0.8661 (tp30) cc_final: 0.8113 (tp30) REVERT: I 82 ARG cc_start: 0.8267 (tmm160) cc_final: 0.8052 (ttp80) REVERT: I 114 GLN cc_start: 0.9357 (mt0) cc_final: 0.8752 (mp10) REVERT: J 164 TYR cc_start: 0.8879 (t80) cc_final: 0.8545 (t80) REVERT: P 66 MET cc_start: 0.9030 (tpt) cc_final: 0.8742 (tpt) REVERT: P 215 MET cc_start: 0.8577 (mtt) cc_final: 0.8318 (mtt) REVERT: Q 51 ASP cc_start: 0.8934 (m-30) cc_final: 0.8409 (m-30) REVERT: Q 144 MET cc_start: 0.8650 (ttm) cc_final: 0.8121 (ttm) REVERT: Q 179 GLN cc_start: 0.7852 (tp40) cc_final: 0.7452 (tp40) REVERT: R 35 GLU cc_start: 0.8791 (pt0) cc_final: 0.8010 (tt0) REVERT: R 41 SER cc_start: 0.9180 (t) cc_final: 0.8974 (p) REVERT: R 66 MET cc_start: 0.8750 (mmm) cc_final: 0.8486 (mmm) REVERT: R 76 GLU cc_start: 0.8750 (tp30) cc_final: 0.8427 (tp30) REVERT: R 114 GLN cc_start: 0.9300 (mt0) cc_final: 0.8686 (mp10) REVERT: S 164 TYR cc_start: 0.8954 (t80) cc_final: 0.8316 (t80) REVERT: S 214 MET cc_start: 0.9027 (mtp) cc_final: 0.8816 (mtt) REVERT: W 51 ASP cc_start: 0.8999 (m-30) cc_final: 0.8464 (m-30) REVERT: W 67 GLN cc_start: 0.8668 (tp40) cc_final: 0.8281 (tp40) REVERT: W 185 MET cc_start: 0.8810 (mtm) cc_final: 0.8225 (mtp) REVERT: X 35 GLU cc_start: 0.8733 (pt0) cc_final: 0.8042 (tt0) REVERT: X 114 GLN cc_start: 0.9348 (mt0) cc_final: 0.8717 (mp10) REVERT: 0 164 TYR cc_start: 0.8953 (t80) cc_final: 0.8470 (t80) REVERT: 3 66 MET cc_start: 0.8884 (tpt) cc_final: 0.8350 (tpp) outliers start: 78 outliers final: 36 residues processed: 517 average time/residue: 0.3071 time to fit residues: 250.9932 Evaluate side-chains 454 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 417 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 32 PHE 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 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 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 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: 2.9990 chunk 245 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.076037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.056993 restraints weight = 82863.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.058639 restraints weight = 50409.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.059670 restraints weight = 37328.984| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 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 = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22690 Z= 0.125 Angle : 0.554 10.384 31140 Z= 0.277 Chirality : 0.039 0.192 3730 Planarity : 0.005 0.053 3980 Dihedral : 4.958 54.617 3183 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.86 % Allowed : 16.30 % Favored : 80.84 % 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: 1.73 (0.11), residues: 2100 sheet: None (None), residues: 0 loop : 1.13 (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 R 84 PHE 0.010 0.001 PHE V 40 TYR 0.022 0.001 TYR Q 164 ARG 0.011 0.001 ARG H 82 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 1420) hydrogen bonds : angle 4.03010 ( 4185) covalent geometry : bond 0.00292 (22690) covalent geometry : angle 0.55421 (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 514 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 453 time to evaluate : 2.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8915 (m-30) cc_final: 0.8313 (m-30) REVERT: L 143 ARG cc_start: 0.9177 (tpt90) cc_final: 0.8427 (tpm170) REVERT: L 144 MET cc_start: 0.8706 (ttm) cc_final: 0.8354 (ttm) REVERT: L 214 MET cc_start: 0.8960 (mtm) cc_final: 0.8593 (mtp) REVERT: M 35 GLU cc_start: 0.8712 (pt0) cc_final: 0.8236 (tt0) REVERT: M 76 GLU cc_start: 0.8689 (tp30) cc_final: 0.8436 (tp30) REVERT: N 164 TYR cc_start: 0.8961 (t80) cc_final: 0.8314 (t80) REVERT: N 192 GLN cc_start: 0.8922 (tp40) cc_final: 0.8577 (tp-100) REVERT: N 215 MET cc_start: 0.8975 (ttm) cc_final: 0.8471 (ttp) REVERT: B 51 ASP cc_start: 0.8901 (m-30) cc_final: 0.8298 (m-30) REVERT: C 32 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7840 (m-80) REVERT: C 35 GLU cc_start: 0.8763 (pt0) cc_final: 0.7997 (tt0) REVERT: C 76 GLU cc_start: 0.8636 (tp30) cc_final: 0.8165 (tp30) REVERT: C 114 GLN cc_start: 0.9332 (mt0) cc_final: 0.8749 (mp10) REVERT: D 164 TYR cc_start: 0.8915 (t80) cc_final: 0.8107 (t80) REVERT: D 171 THR cc_start: 0.9199 (m) cc_final: 0.8898 (p) REVERT: D 192 GLN cc_start: 0.8955 (tp40) cc_final: 0.8648 (tp-100) REVERT: G 55 MET cc_start: 0.9011 (mtp) cc_final: 0.8706 (mtp) REVERT: H 51 ASP cc_start: 0.9066 (m-30) cc_final: 0.8398 (m-30) REVERT: H 164 TYR cc_start: 0.8879 (t80) cc_final: 0.8458 (t80) REVERT: I 76 GLU cc_start: 0.8701 (tp30) cc_final: 0.8142 (tp30) REVERT: I 114 GLN cc_start: 0.9379 (mt0) cc_final: 0.8915 (mp10) REVERT: J 164 TYR cc_start: 0.8887 (t80) cc_final: 0.8453 (t80) REVERT: P 44 SER cc_start: 0.8797 (m) cc_final: 0.8398 (p) REVERT: P 66 MET cc_start: 0.8990 (tpt) cc_final: 0.8682 (tpt) REVERT: P 109 SER cc_start: 0.7087 (OUTLIER) cc_final: 0.6717 (m) REVERT: Q 51 ASP cc_start: 0.8920 (m-30) cc_final: 0.8441 (m-30) REVERT: R 35 GLU cc_start: 0.8814 (pt0) cc_final: 0.8035 (tp30) REVERT: R 41 SER cc_start: 0.9181 (t) cc_final: 0.8967 (p) REVERT: R 76 GLU cc_start: 0.8725 (tp30) cc_final: 0.8404 (tp30) REVERT: R 114 GLN cc_start: 0.9343 (mt0) cc_final: 0.8760 (mp10) REVERT: S 164 TYR cc_start: 0.8954 (t80) cc_final: 0.8372 (t80) REVERT: V 57 ASN cc_start: 0.9084 (m-40) cc_final: 0.8417 (t0) REVERT: V 109 SER cc_start: 0.7353 (OUTLIER) cc_final: 0.6985 (m) REVERT: W 51 ASP cc_start: 0.8993 (m-30) cc_final: 0.8462 (m-30) REVERT: W 67 GLN cc_start: 0.8630 (tp40) cc_final: 0.8290 (tp40) REVERT: W 185 MET cc_start: 0.8804 (mtm) cc_final: 0.8226 (mtp) REVERT: X 35 GLU cc_start: 0.8682 (pt0) cc_final: 0.8003 (tt0) REVERT: X 114 GLN cc_start: 0.9361 (mt0) cc_final: 0.8783 (mp10) REVERT: 0 164 TYR cc_start: 0.8941 (t80) cc_final: 0.8415 (t80) REVERT: 3 185 MET cc_start: 0.9156 (mtm) cc_final: 0.8931 (mtm) outliers start: 61 outliers final: 39 residues processed: 498 average time/residue: 0.3043 time to fit residues: 239.4152 Evaluate side-chains 461 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 419 time to evaluate : 2.438 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain 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 144 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain 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 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 X residue 33 SER Chi-restraints excluded: chain X residue 144 MET 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 Chi-restraints excluded: chain 3 residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 181 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** R 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 195 ASN 2 319 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.076103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.057009 restraints weight = 83592.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.058666 restraints weight = 50667.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059736 restraints weight = 37469.773| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 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 = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22690 Z= 0.122 Angle : 0.562 11.176 31140 Z= 0.276 Chirality : 0.039 0.196 3730 Planarity : 0.005 0.053 3980 Dihedral : 4.754 54.513 3174 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.86 % Allowed : 17.75 % Favored : 79.39 % 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: 2.28 (0.15), residues: 2985 helix: 1.78 (0.11), residues: 2100 sheet: None (None), residues: 0 loop : 1.10 (0.22), residues: 885 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 B 40 TYR 0.024 0.001 TYR Q 164 ARG 0.008 0.001 ARG H 143 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 1420) hydrogen bonds : angle 3.95076 ( 4185) covalent geometry : bond 0.00289 (22690) covalent geometry : angle 0.56154 (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 512 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 451 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9552 (ttmm) cc_final: 0.9345 (tppp) REVERT: L 51 ASP cc_start: 0.8876 (m-30) cc_final: 0.8273 (m-30) REVERT: L 144 MET cc_start: 0.8717 (ttm) cc_final: 0.8322 (ttm) REVERT: M 35 GLU cc_start: 0.8711 (pt0) cc_final: 0.8245 (tt0) REVERT: M 76 GLU cc_start: 0.8695 (tp30) cc_final: 0.8433 (tp30) REVERT: N 164 TYR cc_start: 0.8946 (t80) cc_final: 0.8319 (t80) REVERT: N 192 GLN cc_start: 0.8931 (tp40) cc_final: 0.8580 (tp-100) REVERT: N 215 MET cc_start: 0.8994 (ttm) cc_final: 0.8560 (ttp) REVERT: A 215 MET cc_start: 0.8922 (mtp) cc_final: 0.8575 (mtt) REVERT: B 51 ASP cc_start: 0.8896 (m-30) cc_final: 0.8293 (m-30) REVERT: C 32 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: C 35 GLU cc_start: 0.8737 (pt0) cc_final: 0.7993 (tt0) REVERT: C 76 GLU cc_start: 0.8687 (tp30) cc_final: 0.8214 (tp30) REVERT: C 114 GLN cc_start: 0.9362 (mt0) cc_final: 0.8869 (mp10) REVERT: D 164 TYR cc_start: 0.8901 (t80) cc_final: 0.8067 (t80) REVERT: D 171 THR cc_start: 0.9212 (m) cc_final: 0.8901 (p) REVERT: D 192 GLN cc_start: 0.8963 (tp40) cc_final: 0.8749 (tp-100) REVERT: G 57 ASN cc_start: 0.9124 (m-40) cc_final: 0.8433 (t0) REVERT: H 51 ASP cc_start: 0.9040 (m-30) cc_final: 0.8395 (m-30) REVERT: I 76 GLU cc_start: 0.8725 (tp30) cc_final: 0.8253 (tp30) REVERT: I 114 GLN cc_start: 0.9371 (mt0) cc_final: 0.8946 (mp10) REVERT: J 164 TYR cc_start: 0.8889 (t80) cc_final: 0.8477 (t80) REVERT: P 44 SER cc_start: 0.8809 (m) cc_final: 0.8397 (p) REVERT: P 109 SER cc_start: 0.7205 (OUTLIER) cc_final: 0.6829 (m) REVERT: Q 51 ASP cc_start: 0.8926 (m-30) cc_final: 0.8482 (m-30) REVERT: R 35 GLU cc_start: 0.8803 (pt0) cc_final: 0.8068 (tp30) REVERT: R 50 GLN cc_start: 0.9323 (mt0) cc_final: 0.9105 (mt0) REVERT: R 76 GLU cc_start: 0.8784 (tp30) cc_final: 0.8351 (tp30) REVERT: R 82 ARG cc_start: 0.8196 (tmm160) cc_final: 0.7942 (ttp80) REVERT: R 102 SER cc_start: 0.8767 (t) cc_final: 0.8560 (t) REVERT: R 114 GLN cc_start: 0.9374 (mt0) cc_final: 0.8915 (mp10) REVERT: S 164 TYR cc_start: 0.8960 (t80) cc_final: 0.8376 (t80) REVERT: S 192 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8725 (tp-100) REVERT: U 317 PRO cc_start: 0.9542 (Cg_exo) cc_final: 0.9197 (Cg_endo) REVERT: V 44 SER cc_start: 0.8746 (m) cc_final: 0.8325 (p) REVERT: V 57 ASN cc_start: 0.9076 (m-40) cc_final: 0.8418 (t0) REVERT: W 51 ASP cc_start: 0.8965 (m-30) cc_final: 0.8444 (m-30) REVERT: W 67 GLN cc_start: 0.8642 (tp40) cc_final: 0.8319 (tp40) REVERT: W 185 MET cc_start: 0.8800 (mtm) cc_final: 0.8217 (mtp) REVERT: X 35 GLU cc_start: 0.8673 (pt0) cc_final: 0.7990 (tt0) REVERT: X 114 GLN cc_start: 0.9369 (mt0) cc_final: 0.8794 (mp10) REVERT: 0 164 TYR cc_start: 0.8954 (t80) cc_final: 0.8415 (t80) REVERT: 0 202 LEU cc_start: 0.8973 (tp) cc_final: 0.8727 (tp) outliers start: 61 outliers final: 42 residues processed: 495 average time/residue: 0.3079 time to fit residues: 242.3702 Evaluate side-chains 469 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 425 time to evaluate : 2.538 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 VAL 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 C residue 110 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain 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 27 VAL 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 R residue 110 THR 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 3 residue 16 SER Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 21 optimal weight: 10.0000 chunk 149 optimal weight: 0.0670 chunk 74 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- 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 219 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 179 GLN X 67 GLN 0 193 ASN 2 319 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.056778 restraints weight = 83788.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.058393 restraints weight = 51455.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059438 restraints weight = 38340.220| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 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 = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22690 Z= 0.139 Angle : 0.575 11.210 31140 Z= 0.284 Chirality : 0.039 0.202 3730 Planarity : 0.005 0.053 3980 Dihedral : 4.662 54.501 3169 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.00 % Allowed : 18.41 % 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: 2.28 (0.15), residues: 2985 helix: 1.78 (0.11), residues: 2095 sheet: None (None), residues: 0 loop : 1.10 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 133 HIS 0.002 0.000 HIS P 62 PHE 0.012 0.001 PHE V 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 0.03770 ( 1420) hydrogen bonds : angle 3.98543 ( 4185) covalent geometry : bond 0.00333 (22690) covalent geometry : angle 0.57517 (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 501 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 437 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9567 (ttmm) cc_final: 0.9357 (tppp) REVERT: L 51 ASP cc_start: 0.8901 (m-30) cc_final: 0.8290 (m-30) REVERT: L 55 MET cc_start: 0.9062 (tmm) cc_final: 0.8820 (tmm) REVERT: L 144 MET cc_start: 0.8741 (ttm) cc_final: 0.8222 (ttm) REVERT: M 35 GLU cc_start: 0.8790 (pt0) cc_final: 0.8217 (tt0) REVERT: M 76 GLU cc_start: 0.8744 (tp30) cc_final: 0.8471 (tp30) REVERT: N 164 TYR cc_start: 0.8966 (t80) cc_final: 0.8298 (t80) REVERT: N 192 GLN cc_start: 0.8948 (tp40) cc_final: 0.8597 (tp-100) REVERT: N 215 MET cc_start: 0.9024 (ttm) cc_final: 0.8611 (ttp) REVERT: A 44 SER cc_start: 0.8927 (m) cc_final: 0.8393 (p) REVERT: A 57 ASN cc_start: 0.9085 (m-40) cc_final: 0.8417 (t0) REVERT: A 195 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8541 (p0) REVERT: B 51 ASP cc_start: 0.8908 (m-30) cc_final: 0.8291 (m-30) REVERT: C 32 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: C 35 GLU cc_start: 0.8739 (pt0) cc_final: 0.7987 (tt0) REVERT: C 76 GLU cc_start: 0.8758 (tp30) cc_final: 0.8239 (tp30) REVERT: C 114 GLN cc_start: 0.9372 (mt0) cc_final: 0.8944 (mp10) REVERT: D 171 THR cc_start: 0.9252 (m) cc_final: 0.8938 (p) REVERT: D 173 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8461 (ttp-170) REVERT: D 192 GLN cc_start: 0.9068 (tp40) cc_final: 0.8755 (tp-100) REVERT: G 44 SER cc_start: 0.8847 (m) cc_final: 0.8206 (p) REVERT: G 55 MET cc_start: 0.9145 (mtp) cc_final: 0.8800 (mtp) REVERT: G 57 ASN cc_start: 0.9121 (m-40) cc_final: 0.8447 (t0) REVERT: H 51 ASP cc_start: 0.9048 (m-30) cc_final: 0.8402 (m-30) REVERT: H 66 MET cc_start: 0.8388 (mmm) cc_final: 0.8153 (mmm) REVERT: H 164 TYR cc_start: 0.8827 (t80) cc_final: 0.8497 (t80) REVERT: I 76 GLU cc_start: 0.8739 (tp30) cc_final: 0.8318 (tp30) REVERT: I 114 GLN cc_start: 0.9363 (mt0) cc_final: 0.8951 (mp10) REVERT: J 164 TYR cc_start: 0.8913 (t80) cc_final: 0.8464 (t80) REVERT: P 44 SER cc_start: 0.8829 (m) cc_final: 0.8395 (p) REVERT: Q 51 ASP cc_start: 0.8942 (m-30) cc_final: 0.8485 (m-30) REVERT: R 35 GLU cc_start: 0.8838 (pt0) cc_final: 0.8027 (tp30) REVERT: R 76 GLU cc_start: 0.8836 (tp30) cc_final: 0.8347 (tp30) REVERT: R 114 GLN cc_start: 0.9391 (mt0) cc_final: 0.8951 (mp10) REVERT: S 164 TYR cc_start: 0.8993 (t80) cc_final: 0.8405 (t80) REVERT: S 192 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8740 (tp-100) REVERT: S 215 MET cc_start: 0.9004 (ttm) cc_final: 0.8535 (ttp) REVERT: U 317 PRO cc_start: 0.9542 (Cg_exo) cc_final: 0.9204 (Cg_endo) REVERT: V 44 SER cc_start: 0.8813 (m) cc_final: 0.8382 (p) REVERT: V 57 ASN cc_start: 0.9088 (m-40) cc_final: 0.8408 (t0) REVERT: W 51 ASP cc_start: 0.8974 (m-30) cc_final: 0.8393 (m-30) REVERT: W 67 GLN cc_start: 0.8662 (tp40) cc_final: 0.8430 (tp40) REVERT: W 176 GLN cc_start: 0.8376 (mt0) cc_final: 0.8161 (mt0) REVERT: X 35 GLU cc_start: 0.8666 (pt0) cc_final: 0.7987 (tt0) REVERT: X 114 GLN cc_start: 0.9351 (mt0) cc_final: 0.8774 (mp10) REVERT: 0 164 TYR cc_start: 0.8999 (t80) cc_final: 0.8447 (t80) REVERT: 3 111 LEU cc_start: 0.9293 (tp) cc_final: 0.9072 (mt) outliers start: 64 outliers final: 47 residues processed: 488 average time/residue: 0.2975 time to fit residues: 230.7866 Evaluate side-chains 470 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 421 time to evaluate : 2.689 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 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 C residue 110 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 110 THR 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 W residue 58 THR Chi-restraints excluded: chain W residue 179 GLN 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 144 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 3 residue 16 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 174 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 240 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 63 GLN R 50 GLN X 67 GLN 2 319 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.056333 restraints weight = 83179.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057912 restraints weight = 51350.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.058938 restraints weight = 38466.944| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 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 = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 22690 Z= 0.163 Angle : 0.600 12.040 31140 Z= 0.298 Chirality : 0.040 0.207 3730 Planarity : 0.005 0.055 3980 Dihedral : 4.697 53.667 3169 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.86 % Allowed : 19.48 % Favored : 77.66 % 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: 2.21 (0.15), residues: 2985 helix: 1.72 (0.11), residues: 2095 sheet: None (None), residues: 0 loop : 1.07 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 133 HIS 0.002 0.000 HIS R 84 PHE 0.012 0.001 PHE V 40 TYR 0.033 0.001 TYR Q 164 ARG 0.009 0.001 ARG M 82 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 1420) hydrogen bonds : angle 4.08955 ( 4185) covalent geometry : bond 0.00390 (22690) covalent geometry : angle 0.59993 (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 487 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 426 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9553 (ttmm) cc_final: 0.9341 (tppp) REVERT: L 51 ASP cc_start: 0.8920 (m-30) cc_final: 0.8340 (m-30) REVERT: L 143 ARG cc_start: 0.9211 (tpt90) cc_final: 0.8751 (tpm170) REVERT: L 144 MET cc_start: 0.8618 (ttm) cc_final: 0.8216 (ttm) REVERT: L 176 GLN cc_start: 0.8124 (mt0) cc_final: 0.7870 (mt0) REVERT: M 35 GLU cc_start: 0.8768 (pt0) cc_final: 0.8216 (tt0) REVERT: M 76 GLU cc_start: 0.8805 (tp30) cc_final: 0.8550 (tp30) REVERT: N 164 TYR cc_start: 0.8957 (t80) cc_final: 0.8282 (t80) REVERT: N 192 GLN cc_start: 0.8962 (tp40) cc_final: 0.8606 (tp-100) REVERT: N 205 LEU cc_start: 0.8897 (tp) cc_final: 0.8692 (tt) REVERT: N 215 MET cc_start: 0.8983 (ttm) cc_final: 0.8654 (ttp) REVERT: A 44 SER cc_start: 0.8907 (m) cc_final: 0.8416 (p) REVERT: A 195 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8518 (p0) REVERT: B 51 ASP cc_start: 0.8907 (m-30) cc_final: 0.8277 (m-30) REVERT: C 32 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: C 35 GLU cc_start: 0.8714 (pt0) cc_final: 0.7968 (tt0) REVERT: C 76 GLU cc_start: 0.8750 (tp30) cc_final: 0.8399 (tp30) REVERT: C 114 GLN cc_start: 0.9366 (mt0) cc_final: 0.8949 (mp10) REVERT: D 171 THR cc_start: 0.9310 (m) cc_final: 0.8986 (p) REVERT: D 173 ARG cc_start: 0.8718 (ttp80) cc_final: 0.8489 (ttp-170) REVERT: D 192 GLN cc_start: 0.9076 (tp40) cc_final: 0.8760 (tp-100) REVERT: G 44 SER cc_start: 0.8913 (m) cc_final: 0.8310 (p) REVERT: G 55 MET cc_start: 0.9190 (mtp) cc_final: 0.8844 (mtp) REVERT: G 57 ASN cc_start: 0.9117 (m-40) cc_final: 0.8432 (t0) REVERT: H 51 ASP cc_start: 0.9027 (m-30) cc_final: 0.8409 (m-30) REVERT: H 164 TYR cc_start: 0.8884 (t80) cc_final: 0.8519 (t80) REVERT: I 76 GLU cc_start: 0.8737 (tp30) cc_final: 0.8332 (tp30) REVERT: I 114 GLN cc_start: 0.9372 (mt0) cc_final: 0.8978 (mp10) REVERT: J 164 TYR cc_start: 0.8868 (t80) cc_final: 0.8460 (t80) REVERT: P 44 SER cc_start: 0.8873 (m) cc_final: 0.8303 (p) REVERT: Q 51 ASP cc_start: 0.8949 (m-30) cc_final: 0.8496 (m-30) REVERT: R 35 GLU cc_start: 0.8843 (pt0) cc_final: 0.8017 (tp30) REVERT: R 76 GLU cc_start: 0.8841 (tp30) cc_final: 0.8377 (tp30) REVERT: R 114 GLN cc_start: 0.9348 (mt0) cc_final: 0.8960 (mp10) REVERT: S 164 TYR cc_start: 0.9003 (t80) cc_final: 0.8409 (t80) REVERT: S 192 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8715 (tp-100) REVERT: U 317 PRO cc_start: 0.9547 (Cg_exo) cc_final: 0.9261 (Cg_endo) REVERT: V 44 SER cc_start: 0.8902 (m) cc_final: 0.8478 (p) REVERT: V 57 ASN cc_start: 0.9094 (m-40) cc_final: 0.8399 (t0) REVERT: W 51 ASP cc_start: 0.8956 (m-30) cc_final: 0.8378 (m-30) REVERT: W 176 GLN cc_start: 0.8397 (mt0) cc_final: 0.8176 (mt0) REVERT: X 35 GLU cc_start: 0.8645 (pt0) cc_final: 0.7966 (tt0) REVERT: 0 164 TYR cc_start: 0.9025 (t80) cc_final: 0.8486 (t80) REVERT: 0 193 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7528 (t0) outliers start: 61 outliers final: 48 residues processed: 473 average time/residue: 0.2956 time to fit residues: 223.8408 Evaluate side-chains 468 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 417 time to evaluate : 2.576 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 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 C residue 110 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 27 VAL 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 R residue 110 THR 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 W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 67 GLN Chi-restraints excluded: chain X residue 110 THR 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 3 residue 16 SER Chi-restraints excluded: chain 3 residue 27 VAL 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: 0.8980 chunk 38 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 253 optimal weight: 0.5980 chunk 251 optimal weight: 1.9990 chunk 281 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN ** 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 219 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 193 ASN 2 319 GLN 3 155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.056153 restraints weight = 84256.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057748 restraints weight = 51963.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058769 restraints weight = 38874.789| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 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 = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 22690 Z= 0.162 Angle : 0.612 12.919 31140 Z= 0.304 Chirality : 0.040 0.215 3730 Planarity : 0.005 0.054 3980 Dihedral : 4.750 53.530 3169 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.00 % Allowed : 19.34 % Favored : 77.66 % 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: 2.16 (0.15), residues: 2985 helix: 1.68 (0.11), residues: 2095 sheet: None (None), residues: 0 loop : 1.06 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 0 184 HIS 0.002 0.000 HIS C 84 PHE 0.011 0.001 PHE 3 40 TYR 0.036 0.002 TYR Q 164 ARG 0.010 0.001 ARG X 82 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 1420) hydrogen bonds : angle 4.12382 ( 4185) covalent geometry : bond 0.00397 (22690) covalent geometry : angle 0.61234 (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 488 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 424 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9561 (ttmm) cc_final: 0.9342 (tppp) REVERT: L 51 ASP cc_start: 0.8928 (m-30) cc_final: 0.8355 (m-30) REVERT: L 55 MET cc_start: 0.9054 (tmm) cc_final: 0.8827 (tmm) REVERT: L 143 ARG cc_start: 0.9231 (tpt90) cc_final: 0.8748 (tpm170) REVERT: L 144 MET cc_start: 0.8601 (ttm) cc_final: 0.8112 (ttm) REVERT: L 176 GLN cc_start: 0.8076 (mt0) cc_final: 0.7819 (mt0) REVERT: M 35 GLU cc_start: 0.8781 (pt0) cc_final: 0.8231 (tt0) REVERT: N 164 TYR cc_start: 0.8974 (t80) cc_final: 0.8287 (t80) REVERT: N 192 GLN cc_start: 0.8974 (tp40) cc_final: 0.8615 (tp-100) REVERT: N 205 LEU cc_start: 0.8920 (tp) cc_final: 0.8702 (tt) REVERT: N 215 MET cc_start: 0.9099 (ttm) cc_final: 0.8678 (ttp) REVERT: A 44 SER cc_start: 0.8939 (m) cc_final: 0.8419 (p) REVERT: A 195 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8480 (p0) REVERT: B 25 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9321 (ttmm) REVERT: B 51 ASP cc_start: 0.8912 (m-30) cc_final: 0.8328 (m-30) REVERT: C 32 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: C 35 GLU cc_start: 0.8753 (pt0) cc_final: 0.8012 (tt0) REVERT: C 76 GLU cc_start: 0.8727 (tp30) cc_final: 0.8366 (tp30) REVERT: C 114 GLN cc_start: 0.9382 (mt0) cc_final: 0.8956 (mp10) REVERT: D 171 THR cc_start: 0.9297 (m) cc_final: 0.8983 (p) REVERT: D 192 GLN cc_start: 0.9100 (tp40) cc_final: 0.8792 (tp-100) REVERT: G 44 SER cc_start: 0.8930 (m) cc_final: 0.8305 (p) REVERT: G 57 ASN cc_start: 0.9129 (m-40) cc_final: 0.8492 (t0) REVERT: G 185 MET cc_start: 0.8753 (mtp) cc_final: 0.8319 (mtp) REVERT: H 51 ASP cc_start: 0.9025 (m-30) cc_final: 0.8412 (m-30) REVERT: H 55 MET cc_start: 0.8977 (tmm) cc_final: 0.8718 (tmm) REVERT: H 66 MET cc_start: 0.8498 (mmm) cc_final: 0.8267 (mmm) REVERT: H 143 ARG cc_start: 0.9198 (tpt90) cc_final: 0.8652 (tpm170) REVERT: I 66 MET cc_start: 0.8296 (mmm) cc_final: 0.7966 (mmm) REVERT: I 76 GLU cc_start: 0.8720 (tp30) cc_final: 0.8314 (tp30) REVERT: I 114 GLN cc_start: 0.9382 (mt0) cc_final: 0.8981 (mp10) REVERT: J 164 TYR cc_start: 0.8881 (t80) cc_final: 0.8464 (t80) REVERT: P 44 SER cc_start: 0.8913 (m) cc_final: 0.8329 (p) REVERT: Q 51 ASP cc_start: 0.8959 (m-30) cc_final: 0.8502 (m-30) REVERT: Q 143 ARG cc_start: 0.9304 (tpt90) cc_final: 0.8860 (tpm170) REVERT: R 35 GLU cc_start: 0.8841 (pt0) cc_final: 0.8025 (tp30) REVERT: R 76 GLU cc_start: 0.8839 (tp30) cc_final: 0.8414 (tp30) REVERT: R 114 GLN cc_start: 0.9329 (mt0) cc_final: 0.8967 (mp10) REVERT: S 164 TYR cc_start: 0.9008 (t80) cc_final: 0.8396 (t80) REVERT: S 192 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8690 (tp-100) REVERT: U 317 PRO cc_start: 0.9500 (Cg_exo) cc_final: 0.9215 (Cg_endo) REVERT: V 44 SER cc_start: 0.8938 (m) cc_final: 0.8499 (p) REVERT: V 57 ASN cc_start: 0.9105 (m-40) cc_final: 0.8429 (t0) REVERT: W 51 ASP cc_start: 0.8966 (m-30) cc_final: 0.8382 (m-30) REVERT: W 176 GLN cc_start: 0.8406 (mt0) cc_final: 0.8190 (mt0) REVERT: X 35 GLU cc_start: 0.8656 (pt0) cc_final: 0.7925 (tt0) REVERT: 0 164 TYR cc_start: 0.9050 (t80) cc_final: 0.8486 (t80) REVERT: 3 102 SER cc_start: 0.8944 (m) cc_final: 0.8657 (t) outliers start: 64 outliers final: 49 residues processed: 474 average time/residue: 0.2930 time to fit residues: 222.8190 Evaluate side-chains 467 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 415 time to evaluate : 2.347 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 25 LYS 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 C residue 110 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 27 VAL 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 R residue 110 THR Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 215 MET Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 36 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 260 optimal weight: 0.0870 chunk 204 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- 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** ** M 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.055549 restraints weight = 84380.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.057126 restraints weight = 52336.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.058142 restraints weight = 39233.649| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22690 Z= 0.188 Angle : 0.648 12.474 31140 Z= 0.322 Chirality : 0.041 0.219 3730 Planarity : 0.005 0.056 3980 Dihedral : 4.844 56.490 3169 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.81 % Allowed : 20.00 % Favored : 77.19 % 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: 2.12 (0.15), residues: 2985 helix: 1.64 (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 0.006 0.001 TRP 0 184 HIS 0.002 0.000 HIS Q 62 PHE 0.017 0.002 PHE Z 321 TYR 0.037 0.002 TYR Q 164 ARG 0.009 0.001 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 1420) hydrogen bonds : angle 4.25008 ( 4185) covalent geometry : bond 0.00456 (22690) covalent geometry : angle 0.64834 (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 482 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 422 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 25 LYS cc_start: 0.9552 (ttmm) cc_final: 0.9331 (tppp) REVERT: L 51 ASP cc_start: 0.8922 (m-30) cc_final: 0.8358 (m-30) REVERT: L 55 MET cc_start: 0.9090 (tmm) cc_final: 0.8864 (tmm) REVERT: L 144 MET cc_start: 0.8608 (ttm) cc_final: 0.8068 (ttm) REVERT: M 35 GLU cc_start: 0.8779 (pt0) cc_final: 0.8277 (tt0) REVERT: M 76 GLU cc_start: 0.8599 (tp30) cc_final: 0.8348 (tp30) REVERT: N 164 TYR cc_start: 0.8986 (t80) cc_final: 0.8283 (t80) REVERT: N 192 GLN cc_start: 0.8930 (tp40) cc_final: 0.8566 (tp-100) REVERT: N 205 LEU cc_start: 0.8909 (tp) cc_final: 0.8689 (tt) REVERT: N 215 MET cc_start: 0.9030 (ttm) cc_final: 0.8616 (ttp) REVERT: A 44 SER cc_start: 0.8895 (m) cc_final: 0.8429 (p) REVERT: B 25 LYS cc_start: 0.9536 (OUTLIER) cc_final: 0.9324 (ttmm) REVERT: B 51 ASP cc_start: 0.8923 (m-30) cc_final: 0.8348 (m-30) REVERT: C 32 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: C 35 GLU cc_start: 0.8724 (pt0) cc_final: 0.8003 (tt0) REVERT: C 76 GLU cc_start: 0.8743 (tp30) cc_final: 0.8400 (tp30) REVERT: C 114 GLN cc_start: 0.9401 (mt0) cc_final: 0.8978 (mp10) REVERT: D 171 THR cc_start: 0.9324 (m) cc_final: 0.9060 (p) REVERT: D 173 ARG cc_start: 0.8788 (ttp80) cc_final: 0.8566 (ttp-170) REVERT: D 192 GLN cc_start: 0.9090 (tp40) cc_final: 0.8785 (tp-100) REVERT: G 44 SER cc_start: 0.8975 (m) cc_final: 0.8367 (p) REVERT: G 57 ASN cc_start: 0.9133 (m-40) cc_final: 0.8489 (t0) REVERT: G 185 MET cc_start: 0.8740 (mtp) cc_final: 0.8385 (mtp) REVERT: H 44 SER cc_start: 0.9067 (p) cc_final: 0.8759 (p) REVERT: H 51 ASP cc_start: 0.8997 (m-30) cc_final: 0.8367 (m-30) REVERT: H 66 MET cc_start: 0.8542 (mmm) cc_final: 0.8315 (mmm) REVERT: H 176 GLN cc_start: 0.8418 (mt0) cc_final: 0.8170 (mt0) REVERT: H 179 GLN cc_start: 0.7574 (tp40) cc_final: 0.7150 (tp40) REVERT: I 76 GLU cc_start: 0.8712 (tp30) cc_final: 0.8340 (tp30) REVERT: I 114 GLN cc_start: 0.9381 (mt0) cc_final: 0.8981 (mp10) REVERT: J 164 TYR cc_start: 0.8910 (t80) cc_final: 0.8474 (t80) REVERT: P 44 SER cc_start: 0.8988 (m) cc_final: 0.8412 (p) REVERT: Q 51 ASP cc_start: 0.8956 (m-30) cc_final: 0.8500 (m-30) REVERT: Q 118 MET cc_start: 0.7907 (mmm) cc_final: 0.7692 (mmt) REVERT: Q 143 ARG cc_start: 0.9272 (tpt90) cc_final: 0.8866 (tpm170) REVERT: R 35 GLU cc_start: 0.8820 (pt0) cc_final: 0.8013 (tp30) REVERT: R 76 GLU cc_start: 0.8812 (tp30) cc_final: 0.8384 (tp30) REVERT: R 114 GLN cc_start: 0.9333 (mt0) cc_final: 0.8973 (mp10) REVERT: S 164 TYR cc_start: 0.8996 (t80) cc_final: 0.8396 (t80) REVERT: S 192 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8711 (tp-100) REVERT: S 215 MET cc_start: 0.8824 (ttm) cc_final: 0.8390 (ttp) REVERT: U 317 PRO cc_start: 0.9512 (Cg_exo) cc_final: 0.9239 (Cg_endo) REVERT: V 44 SER cc_start: 0.9009 (m) cc_final: 0.8586 (p) REVERT: W 51 ASP cc_start: 0.8984 (m-30) cc_final: 0.8418 (m-30) REVERT: W 176 GLN cc_start: 0.8402 (mt0) cc_final: 0.8174 (mt0) REVERT: X 35 GLU cc_start: 0.8667 (pt0) cc_final: 0.7961 (tt0) REVERT: 0 164 TYR cc_start: 0.9057 (t80) cc_final: 0.8483 (t80) REVERT: 3 102 SER cc_start: 0.8972 (m) cc_final: 0.8683 (t) outliers start: 60 outliers final: 50 residues processed: 472 average time/residue: 0.2954 time to fit residues: 223.7005 Evaluate side-chains 469 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 417 time to evaluate : 2.800 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 25 LYS 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 C residue 110 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR 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 16 SER Chi-restraints excluded: chain P residue 27 VAL 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 R residue 110 THR Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 215 MET Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 49 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 238 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** M 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Q 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 = 0.3266 r_free = 0.3266 target = 0.074398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.055106 restraints weight = 85244.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056670 restraints weight = 52864.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.057691 restraints weight = 39700.337| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 22690 Z= 0.206 Angle : 0.663 11.656 31140 Z= 0.331 Chirality : 0.042 0.250 3730 Planarity : 0.005 0.061 3980 Dihedral : 4.923 58.356 3169 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.53 % Allowed : 20.84 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.00 (0.15), residues: 2985 helix: 1.55 (0.11), residues: 2150 sheet: None (None), residues: 0 loop : 0.99 (0.23), residues: 835 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 0.002 PHE Z 321 TYR 0.038 0.002 TYR Q 164 ARG 0.012 0.001 ARG X 82 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 1420) hydrogen bonds : angle 4.35528 ( 4185) covalent geometry : bond 0.00493 (22690) covalent geometry : angle 0.66288 (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 470 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 416 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8919 (m-30) cc_final: 0.8328 (m-30) REVERT: L 143 ARG cc_start: 0.9184 (tpt90) cc_final: 0.8834 (tpm170) REVERT: L 144 MET cc_start: 0.8616 (ttm) cc_final: 0.8102 (ttm) REVERT: M 35 GLU cc_start: 0.8774 (pt0) cc_final: 0.8259 (tt0) REVERT: M 76 GLU cc_start: 0.8636 (tp30) cc_final: 0.8363 (tp30) REVERT: N 164 TYR cc_start: 0.8988 (t80) cc_final: 0.8271 (t80) REVERT: N 187 GLU cc_start: 0.9217 (mm-30) cc_final: 0.9001 (mm-30) REVERT: N 192 GLN cc_start: 0.8934 (tp40) cc_final: 0.8531 (tp-100) REVERT: N 205 LEU cc_start: 0.8937 (tp) cc_final: 0.8715 (tt) REVERT: N 215 MET cc_start: 0.9066 (ttm) cc_final: 0.8649 (ttp) REVERT: A 44 SER cc_start: 0.8963 (m) cc_final: 0.8508 (p) REVERT: A 102 SER cc_start: 0.8997 (m) cc_final: 0.8675 (t) REVERT: B 25 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9325 (ttmm) REVERT: B 51 ASP cc_start: 0.8923 (m-30) cc_final: 0.8352 (m-30) REVERT: B 67 GLN cc_start: 0.8567 (tp40) cc_final: 0.8285 (tp40) REVERT: B 84 HIS cc_start: 0.8015 (m90) cc_final: 0.7800 (m90) REVERT: B 164 TYR cc_start: 0.8625 (t80) cc_final: 0.8321 (t80) REVERT: C 32 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: C 35 GLU cc_start: 0.8726 (pt0) cc_final: 0.8013 (tt0) REVERT: C 76 GLU cc_start: 0.8722 (tp30) cc_final: 0.8306 (tp30) REVERT: C 114 GLN cc_start: 0.9406 (mt0) cc_final: 0.8962 (mp10) REVERT: D 171 THR cc_start: 0.9327 (m) cc_final: 0.9057 (p) REVERT: D 173 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8594 (ttp-170) REVERT: D 192 GLN cc_start: 0.9095 (tp40) cc_final: 0.8791 (tp-100) REVERT: G 44 SER cc_start: 0.9029 (m) cc_final: 0.8399 (p) REVERT: G 57 ASN cc_start: 0.9140 (m-40) cc_final: 0.8495 (t0) REVERT: G 185 MET cc_start: 0.8738 (mtp) cc_final: 0.8406 (mtp) REVERT: H 44 SER cc_start: 0.9070 (p) cc_final: 0.8763 (p) REVERT: H 51 ASP cc_start: 0.9018 (m-30) cc_final: 0.8401 (m-30) REVERT: H 66 MET cc_start: 0.8546 (mmm) cc_final: 0.8326 (mmm) REVERT: H 143 ARG cc_start: 0.9250 (tpt90) cc_final: 0.8871 (tpm170) REVERT: I 76 GLU cc_start: 0.8710 (tp30) cc_final: 0.8339 (tp30) REVERT: I 114 GLN cc_start: 0.9377 (mt0) cc_final: 0.8964 (mp10) REVERT: J 164 TYR cc_start: 0.8991 (t80) cc_final: 0.8525 (t80) REVERT: P 44 SER cc_start: 0.9055 (m) cc_final: 0.8674 (p) REVERT: Q 51 ASP cc_start: 0.8926 (m-30) cc_final: 0.8457 (m-30) REVERT: Q 143 ARG cc_start: 0.9269 (tpt90) cc_final: 0.8856 (tpm170) REVERT: R 35 GLU cc_start: 0.8829 (pt0) cc_final: 0.8025 (tp30) REVERT: R 76 GLU cc_start: 0.8809 (tp30) cc_final: 0.8389 (tp30) REVERT: R 114 GLN cc_start: 0.9337 (mt0) cc_final: 0.8960 (mp10) REVERT: S 164 TYR cc_start: 0.9019 (t80) cc_final: 0.8430 (t80) REVERT: S 192 GLN cc_start: 0.8946 (tp-100) cc_final: 0.8682 (tp-100) REVERT: S 215 MET cc_start: 0.8833 (ttm) cc_final: 0.8569 (ttp) REVERT: V 44 SER cc_start: 0.9066 (m) cc_final: 0.8658 (p) REVERT: V 57 ASN cc_start: 0.9144 (m-40) cc_final: 0.8413 (t0) REVERT: W 51 ASP cc_start: 0.8976 (m-30) cc_final: 0.8413 (m-30) REVERT: W 176 GLN cc_start: 0.8417 (mt0) cc_final: 0.8200 (mt0) REVERT: X 35 GLU cc_start: 0.8674 (pt0) cc_final: 0.7966 (tt0) REVERT: 0 164 TYR cc_start: 0.9066 (t80) cc_final: 0.8492 (t80) REVERT: 0 215 MET cc_start: 0.9232 (ttm) cc_final: 0.8947 (ttp) REVERT: 3 44 SER cc_start: 0.9057 (m) cc_final: 0.8718 (p) REVERT: 3 102 SER cc_start: 0.8971 (m) cc_final: 0.8674 (t) outliers start: 54 outliers final: 44 residues processed: 460 average time/residue: 0.2977 time to fit residues: 219.6736 Evaluate side-chains 457 residues out of total 2655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 411 time to evaluate : 2.607 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 25 LYS 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 C residue 110 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 193 ASN Chi-restraints excluded: chain P residue 27 VAL 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 R residue 110 THR 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 X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 147 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 239 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 283 optimal weight: 0.6980 chunk 174 optimal weight: 0.0370 chunk 141 optimal weight: 7.9990 chunk 111 optimal weight: 0.0870 overall best weight: 2.5640 ------------------------------------------------------------------------------- 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** ** M 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN H 176 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 ASN ** 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 = 0.3292 r_free = 0.3292 target = 0.075621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.056423 restraints weight = 83729.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.058023 restraints weight = 51403.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.059066 restraints weight = 38371.478| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22690 Z= 0.143 Angle : 0.637 11.086 31140 Z= 0.315 Chirality : 0.041 0.238 3730 Planarity : 0.005 0.065 3980 Dihedral : 4.605 58.496 3163 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.39 % Allowed : 21.12 % Favored : 76.49 % 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: 2.10 (0.16), residues: 2985 helix: 1.62 (0.11), residues: 2120 sheet: None (None), residues: 0 loop : 1.09 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 184 HIS 0.002 0.000 HIS B 62 PHE 0.014 0.001 PHE Z 321 TYR 0.029 0.002 TYR W 164 ARG 0.012 0.001 ARG X 82 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1420) hydrogen bonds : angle 4.12755 ( 4185) covalent geometry : bond 0.00355 (22690) covalent geometry : angle 0.63731 (31140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7473.94 seconds wall clock time: 130 minutes 53.92 seconds (7853.92 seconds total)