Starting phenix.real_space_refine on Sun Apr 7 11:41:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykm_10828/04_2024/6ykm_10828.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykm_10828/04_2024/6ykm_10828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykm_10828/04_2024/6ykm_10828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykm_10828/04_2024/6ykm_10828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykm_10828/04_2024/6ykm_10828.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykm_10828/04_2024/6ykm_10828.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 70 5.16 5 C 6752 2.51 5 N 1688 2.21 5 O 1924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 251": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10434 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "B" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "C" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "D" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "E" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "F" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 328 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "G" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 328 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.65, per 1000 atoms: 0.54 Number of scatterers: 10434 At special positions: 0 Unit cell: (95.68, 114.816, 99.84, 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 70 16.00 O 1924 8.00 N 1688 7.00 C 6752 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 - 3.50 Amino acid : False - 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: 3.67 Conformation dependent library (CDL) restraints added in 2.1 seconds 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 0 sheets defined 83.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.647A pdb=" N MET A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.919A pdb=" N ILE A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.656A pdb=" N LYS A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 73 through 91 Processing helix chain 'A' and resid 93 through 100 Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.662A pdb=" N ASP A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 160 removed outlier: 4.062A pdb=" N GLU A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Proline residue: A 154 - end of helix removed outlier: 3.902A pdb=" N LEU A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 174 through 199 removed outlier: 4.435A pdb=" N ALA A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 229 removed outlier: 3.886A pdb=" N ASP A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'B' and resid 6 through 17 removed outlier: 3.640A pdb=" N ALA B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 32 through 47 removed outlier: 3.532A pdb=" N VAL B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 52 through 62 removed outlier: 3.704A pdb=" N LYS B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.584A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.629A pdb=" N LEU B 96 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.929A pdb=" N GLU B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 103 " --> pdb=" O THR B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 103' Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 120 through 129 removed outlier: 4.031A pdb=" N GLU B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 152 removed outlier: 3.611A pdb=" N GLU B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 143 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 174 through 198 removed outlier: 3.691A pdb=" N MET B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 229 removed outlier: 4.150A pdb=" N ASP B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.518A pdb=" N ALA B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 17 removed outlier: 3.769A pdb=" N LEU C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.656A pdb=" N LEU C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 47 removed outlier: 3.599A pdb=" N ILE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Proline residue: C 41 - end of helix Processing helix chain 'C' and resid 52 through 62 removed outlier: 3.543A pdb=" N LYS C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.554A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.646A pdb=" N GLN C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.736A pdb=" N LEU C 96 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 97 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER C 98 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 3.623A pdb=" N MET C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 129 removed outlier: 3.883A pdb=" N GLU C 126 " --> pdb=" O GLU C 122 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.988A pdb=" N TRP C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'C' and resid 164 through 171 Processing helix chain 'C' and resid 174 through 199 removed outlier: 3.679A pdb=" N THR C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 229 removed outlier: 4.161A pdb=" N ASP C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 214 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'D' and resid 2 through 22 removed outlier: 3.855A pdb=" N MET D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 14 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 22 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 3.568A pdb=" N VAL D 30 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE D 31 " --> pdb=" O LEU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 52 through 62 removed outlier: 3.597A pdb=" N LYS D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.631A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.624A pdb=" N THR D 100 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 120 through 163 removed outlier: 3.784A pdb=" N GLU D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 132 " --> pdb=" O MET D 128 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TRP D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Proline residue: D 154 - end of helix removed outlier: 3.628A pdb=" N LEU D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 171 removed outlier: 3.588A pdb=" N LYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 199 removed outlier: 3.883A pdb=" N ALA D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 190 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 231 removed outlier: 4.080A pdb=" N ASP D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU D 214 " --> pdb=" O ASN D 210 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'E' and resid 2 through 22 removed outlier: 3.519A pdb=" N ILE E 6 " --> pdb=" O ASP E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 3.808A pdb=" N ILE E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 52 through 62 removed outlier: 3.532A pdb=" N LYS E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.615A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 91 removed outlier: 3.781A pdb=" N GLN E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.752A pdb=" N ASN E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 120 through 133 removed outlier: 4.239A pdb=" N GLU E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE E 130 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN E 131 " --> pdb=" O SER E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 143 Processing helix chain 'E' and resid 143 through 152 Processing helix chain 'E' and resid 152 through 171 removed outlier: 3.587A pdb=" N MET E 156 " --> pdb=" O THR E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 185 through 197 Processing helix chain 'E' and resid 199 through 229 removed outlier: 3.972A pdb=" N ASP E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU E 214 " --> pdb=" O ASN E 210 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 216 " --> pdb=" O MET E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 242 Processing helix chain 'E' and resid 243 through 245 No H-bonds generated for 'chain 'E' and resid 243 through 245' Processing helix chain 'F' and resid 16 through 39 removed outlier: 3.850A pdb=" N TYR F 20 " --> pdb=" O TRP F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 53 removed outlier: 3.974A pdb=" N GLU F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 37 Processing helix chain 'G' and resid 43 through 53 removed outlier: 3.833A pdb=" N ALA G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS G 49 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2475 1.33 - 1.45: 1955 1.45 - 1.57: 6064 1.57 - 1.69: 0 1.69 - 1.81: 125 Bond restraints: 10619 Sorted by residual: bond pdb=" C MET E 40 " pdb=" N PRO E 41 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.23e-02 6.61e+03 1.11e+01 bond pdb=" C MET B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.336 1.372 -0.037 1.23e-02 6.61e+03 8.97e+00 bond pdb=" C MET D 40 " pdb=" N PRO D 41 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.23e-02 6.61e+03 8.79e+00 bond pdb=" CG1 ILE A 78 " pdb=" CD1 ILE A 78 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.84e+00 bond pdb=" C VAL F 18 " pdb=" N PRO F 19 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.36e-02 5.41e+03 3.71e+00 ... (remaining 10614 not shown) Histogram of bond angle deviations from ideal: 97.57 - 104.87: 185 104.87 - 112.18: 4937 112.18 - 119.48: 4318 119.48 - 126.78: 4789 126.78 - 134.09: 119 Bond angle restraints: 14348 Sorted by residual: angle pdb=" C SER G 38 " pdb=" N LYS G 39 " pdb=" CA LYS G 39 " ideal model delta sigma weight residual 122.07 127.75 -5.68 1.43e+00 4.89e-01 1.58e+01 angle pdb=" C ALA F 43 " pdb=" N LYS F 44 " pdb=" CA LYS F 44 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C SER C 253 " pdb=" N GLN C 254 " pdb=" CA GLN C 254 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C LEU E 96 " pdb=" N GLU E 97 " pdb=" CA GLU E 97 " ideal model delta sigma weight residual 120.28 124.79 -4.51 1.34e+00 5.57e-01 1.13e+01 angle pdb=" CA LEU B 115 " pdb=" CB LEU B 115 " pdb=" CG LEU B 115 " ideal model delta sigma weight residual 116.30 127.14 -10.84 3.50e+00 8.16e-02 9.59e+00 ... (remaining 14343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 5842 14.14 - 28.28: 401 28.28 - 42.42: 112 42.42 - 56.56: 18 56.56 - 70.70: 3 Dihedral angle restraints: 6376 sinusoidal: 2490 harmonic: 3886 Sorted by residual: dihedral pdb=" CA LEU B 199 " pdb=" C LEU B 199 " pdb=" N PHE B 200 " pdb=" CA PHE B 200 " ideal model delta harmonic sigma weight residual -180.00 -153.27 -26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA LEU E 199 " pdb=" C LEU E 199 " pdb=" N PHE E 200 " pdb=" CA PHE E 200 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA LEU C 199 " pdb=" C LEU C 199 " pdb=" N PHE C 200 " pdb=" CA PHE C 200 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 6373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 934 0.047 - 0.094: 550 0.094 - 0.142: 162 0.142 - 0.189: 29 0.189 - 0.236: 7 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CG LEU C 158 " pdb=" CB LEU C 158 " pdb=" CD1 LEU C 158 " pdb=" CD2 LEU C 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE E 182 " pdb=" CA ILE E 182 " pdb=" CG1 ILE E 182 " pdb=" CG2 ILE E 182 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CG LEU G 28 " pdb=" CB LEU G 28 " pdb=" CD1 LEU G 28 " pdb=" CD2 LEU G 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1679 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 149 " -0.028 2.00e-02 2.50e+03 3.07e-02 1.65e+01 pdb=" CG PHE E 149 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE E 149 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE E 149 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 149 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE E 149 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE E 149 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 149 " 0.030 2.00e-02 2.50e+03 3.06e-02 1.64e+01 pdb=" CG PHE C 149 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE C 149 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE C 149 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 149 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 149 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 149 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 149 " 0.029 2.00e-02 2.50e+03 2.95e-02 1.52e+01 pdb=" CG PHE B 149 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE B 149 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 149 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 149 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 149 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 149 " 0.011 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2487 2.78 - 3.31: 10069 3.31 - 3.84: 17573 3.84 - 4.37: 22131 4.37 - 4.90: 36677 Nonbonded interactions: 88937 Sorted by model distance: nonbonded pdb=" O ILE C 38 " pdb=" OG1 THR C 42 " model vdw 2.256 2.440 nonbonded pdb=" OE2 GLU A 23 " pdb=" OG SER B 34 " model vdw 2.304 2.440 nonbonded pdb=" O HOH B 303 " pdb=" O HOH F 304 " model vdw 2.327 2.440 nonbonded pdb=" OG SER F 25 " pdb=" O HOH F 301 " model vdw 2.343 2.440 nonbonded pdb=" OE2 GLU C 23 " pdb=" OG SER D 34 " model vdw 2.370 2.440 ... (remaining 88932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.910 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.440 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.009 0.095 10619 Z= 0.589 Angle : 1.067 10.840 14348 Z= 0.565 Chirality : 0.061 0.236 1682 Planarity : 0.008 0.062 1804 Dihedral : 11.095 70.703 3862 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.17), residues: 1343 helix: -3.20 (0.11), residues: 1092 sheet: None (None), residues: 0 loop : -1.13 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP F 35 HIS 0.010 0.002 HIS B 52 PHE 0.068 0.005 PHE C 149 TYR 0.045 0.005 TYR C 197 ARG 0.008 0.001 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.646 Fit side-chains REVERT: A 208 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7929 (tttm) REVERT: B 110 ASN cc_start: 0.8038 (p0) cc_final: 0.7680 (m110) REVERT: B 140 LYS cc_start: 0.8163 (ttmp) cc_final: 0.7759 (mtmm) REVERT: B 226 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8303 (ttmm) REVERT: C 40 MET cc_start: 0.8113 (mmt) cc_final: 0.7727 (mmt) REVERT: C 216 LYS cc_start: 0.8497 (tptm) cc_final: 0.7735 (mttt) REVERT: D 151 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7041 (mt-10) REVERT: D 223 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7763 (mm-30) REVERT: D 230 GLU cc_start: 0.7084 (mp0) cc_final: 0.6849 (mt-10) REVERT: E 28 LEU cc_start: 0.7127 (tt) cc_final: 0.6687 (mp) REVERT: E 61 LYS cc_start: 0.8339 (mttp) cc_final: 0.8068 (mtmt) REVERT: E 104 GLU cc_start: 0.7561 (mp0) cc_final: 0.7230 (mm-30) REVERT: E 140 LYS cc_start: 0.8461 (ptpt) cc_final: 0.8012 (pttm) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2697 time to fit residues: 97.9895 Evaluate side-chains 186 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 138 HIS C 52 HIS C 134 GLN D 110 ASN D 134 GLN D 243 ASN E 134 GLN E 138 HIS E 243 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10619 Z= 0.191 Angle : 0.573 6.788 14348 Z= 0.296 Chirality : 0.041 0.140 1682 Planarity : 0.005 0.047 1804 Dihedral : 5.288 22.941 1402 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.26 % Allowed : 8.57 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.21), residues: 1343 helix: -1.65 (0.14), residues: 1093 sheet: None (None), residues: 0 loop : -0.53 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 35 HIS 0.009 0.001 HIS E 138 PHE 0.023 0.002 PHE B 149 TYR 0.019 0.002 TYR C 197 ARG 0.004 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 201 time to evaluate : 1.078 Fit side-chains REVERT: A 208 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7820 (tttm) REVERT: B 140 LYS cc_start: 0.8016 (ttmp) cc_final: 0.7599 (mtmm) REVERT: B 226 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8312 (ttmm) REVERT: D 33 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8454 (tp) REVERT: D 151 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6873 (mt-10) REVERT: E 61 LYS cc_start: 0.8306 (mttp) cc_final: 0.8036 (mtmt) REVERT: E 64 LYS cc_start: 0.7890 (pttm) cc_final: 0.6794 (mmmt) REVERT: E 104 GLU cc_start: 0.7687 (mp0) cc_final: 0.7321 (mm-30) REVERT: E 117 ASP cc_start: 0.8029 (m-30) cc_final: 0.7789 (m-30) REVERT: E 140 LYS cc_start: 0.8451 (ptpt) cc_final: 0.8027 (pttm) outliers start: 25 outliers final: 10 residues processed: 215 average time/residue: 0.2586 time to fit residues: 75.0410 Evaluate side-chains 180 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 138 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 ASN E 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10619 Z= 0.211 Angle : 0.556 8.876 14348 Z= 0.282 Chirality : 0.041 0.128 1682 Planarity : 0.004 0.041 1804 Dihedral : 4.947 22.145 1402 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.08 % Allowed : 11.19 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.22), residues: 1343 helix: -0.98 (0.15), residues: 1100 sheet: None (None), residues: 0 loop : -0.16 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 146 HIS 0.017 0.001 HIS E 138 PHE 0.023 0.002 PHE B 149 TYR 0.020 0.002 TYR C 197 ARG 0.003 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.143 Fit side-chains REVERT: A 208 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7794 (tttm) REVERT: B 110 ASN cc_start: 0.7735 (m-40) cc_final: 0.7468 (m-40) REVERT: B 113 MET cc_start: 0.7802 (ptm) cc_final: 0.7580 (ptp) REVERT: B 140 LYS cc_start: 0.8023 (ttmp) cc_final: 0.7573 (mtmm) REVERT: D 33 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8336 (tp) REVERT: D 151 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6910 (mt-10) REVERT: E 9 MET cc_start: 0.8000 (mtp) cc_final: 0.7789 (mtm) REVERT: E 61 LYS cc_start: 0.8365 (mttp) cc_final: 0.8099 (mtmt) REVERT: E 104 GLU cc_start: 0.7674 (mp0) cc_final: 0.7314 (mm-30) REVERT: E 117 ASP cc_start: 0.8017 (m-30) cc_final: 0.7797 (m-30) REVERT: E 140 LYS cc_start: 0.8395 (ptpt) cc_final: 0.7991 (ptmm) REVERT: E 207 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8257 (tt) outliers start: 23 outliers final: 13 residues processed: 182 average time/residue: 0.2441 time to fit residues: 61.9220 Evaluate side-chains 176 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 128 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10619 Z= 0.173 Angle : 0.520 6.764 14348 Z= 0.265 Chirality : 0.040 0.119 1682 Planarity : 0.004 0.039 1804 Dihedral : 4.649 21.519 1402 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.99 % Allowed : 11.46 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.23), residues: 1343 helix: -0.48 (0.15), residues: 1100 sheet: None (None), residues: 0 loop : -0.17 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 203 HIS 0.003 0.001 HIS B 52 PHE 0.019 0.001 PHE A 149 TYR 0.018 0.002 TYR C 197 ARG 0.006 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: B 110 ASN cc_start: 0.7790 (m-40) cc_final: 0.7539 (m-40) REVERT: B 113 MET cc_start: 0.7724 (ptm) cc_final: 0.7502 (ptp) REVERT: B 140 LYS cc_start: 0.7998 (ttmp) cc_final: 0.7550 (mtmm) REVERT: D 33 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8388 (tp) REVERT: D 151 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7043 (mt-10) REVERT: E 9 MET cc_start: 0.7998 (mtp) cc_final: 0.7786 (mtm) REVERT: E 64 LYS cc_start: 0.7925 (pttm) cc_final: 0.6728 (mmmt) REVERT: E 104 GLU cc_start: 0.7719 (mp0) cc_final: 0.7331 (mm-30) REVERT: E 117 ASP cc_start: 0.7973 (m-30) cc_final: 0.7751 (m-30) REVERT: E 140 LYS cc_start: 0.8278 (ptpt) cc_final: 0.7832 (mtmm) REVERT: E 207 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8260 (tt) outliers start: 22 outliers final: 11 residues processed: 181 average time/residue: 0.2446 time to fit residues: 61.4415 Evaluate side-chains 167 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 115 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN D 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10619 Z= 0.176 Angle : 0.509 6.522 14348 Z= 0.260 Chirality : 0.040 0.117 1682 Planarity : 0.004 0.037 1804 Dihedral : 4.515 21.115 1402 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.26 % Allowed : 12.27 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.23), residues: 1343 helix: -0.15 (0.16), residues: 1103 sheet: None (None), residues: 0 loop : 0.09 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 203 HIS 0.003 0.001 HIS B 52 PHE 0.017 0.001 PHE B 149 TYR 0.016 0.002 TYR C 197 ARG 0.007 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 1.102 Fit side-chains REVERT: B 113 MET cc_start: 0.7666 (ptm) cc_final: 0.7114 (ptt) REVERT: B 140 LYS cc_start: 0.8001 (ttmp) cc_final: 0.7547 (mtmm) REVERT: D 33 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8358 (tp) REVERT: D 151 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7057 (mt-10) REVERT: E 9 MET cc_start: 0.8059 (mtp) cc_final: 0.7828 (mtm) REVERT: E 64 LYS cc_start: 0.7843 (pttm) cc_final: 0.6665 (mmmt) REVERT: E 104 GLU cc_start: 0.7696 (mp0) cc_final: 0.7312 (mm-30) REVERT: E 113 MET cc_start: 0.7968 (ttm) cc_final: 0.7552 (mtp) REVERT: E 117 ASP cc_start: 0.7941 (m-30) cc_final: 0.7702 (m-30) REVERT: E 140 LYS cc_start: 0.8276 (ptpt) cc_final: 0.7835 (mtmm) REVERT: E 207 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8292 (tt) outliers start: 25 outliers final: 18 residues processed: 178 average time/residue: 0.2491 time to fit residues: 61.8975 Evaluate side-chains 175 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10619 Z= 0.180 Angle : 0.509 7.580 14348 Z= 0.258 Chirality : 0.040 0.117 1682 Planarity : 0.004 0.036 1804 Dihedral : 4.453 20.875 1402 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.35 % Allowed : 13.36 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1343 helix: 0.07 (0.16), residues: 1103 sheet: None (None), residues: 0 loop : 0.29 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 146 HIS 0.003 0.001 HIS B 52 PHE 0.017 0.001 PHE B 149 TYR 0.015 0.002 TYR C 197 ARG 0.007 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.226 Fit side-chains REVERT: B 113 MET cc_start: 0.7480 (ptm) cc_final: 0.6959 (ptt) REVERT: B 140 LYS cc_start: 0.8015 (ttmp) cc_final: 0.7516 (mtmm) REVERT: D 33 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8344 (tp) REVERT: D 151 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7083 (mt-10) REVERT: E 9 MET cc_start: 0.8068 (mtp) cc_final: 0.7820 (mtm) REVERT: E 64 LYS cc_start: 0.7825 (pttm) cc_final: 0.6670 (mmmt) REVERT: E 104 GLU cc_start: 0.7687 (mp0) cc_final: 0.7309 (mm-30) REVERT: E 113 MET cc_start: 0.8046 (ttm) cc_final: 0.7718 (mtp) REVERT: E 117 ASP cc_start: 0.7905 (m-30) cc_final: 0.7689 (m-30) REVERT: E 140 LYS cc_start: 0.8279 (ptpt) cc_final: 0.7909 (mtpt) REVERT: E 207 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8300 (tt) outliers start: 26 outliers final: 21 residues processed: 175 average time/residue: 0.2385 time to fit residues: 58.1412 Evaluate side-chains 174 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10619 Z= 0.159 Angle : 0.491 6.734 14348 Z= 0.250 Chirality : 0.039 0.184 1682 Planarity : 0.004 0.037 1804 Dihedral : 4.363 20.658 1402 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.08 % Allowed : 13.45 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1343 helix: 0.39 (0.16), residues: 1083 sheet: None (None), residues: 0 loop : 0.45 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 203 HIS 0.003 0.001 HIS B 52 PHE 0.014 0.001 PHE B 149 TYR 0.014 0.002 TYR D 197 ARG 0.008 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.179 Fit side-chains REVERT: B 113 MET cc_start: 0.7522 (ptm) cc_final: 0.7004 (ptt) REVERT: B 140 LYS cc_start: 0.8004 (ttmp) cc_final: 0.7514 (mtmm) REVERT: D 33 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8322 (tp) REVERT: D 151 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7061 (mt-10) REVERT: E 9 MET cc_start: 0.8047 (mtp) cc_final: 0.7792 (mtm) REVERT: E 64 LYS cc_start: 0.7788 (pttm) cc_final: 0.6643 (mmmt) REVERT: E 104 GLU cc_start: 0.7687 (mp0) cc_final: 0.7305 (mm-30) REVERT: E 113 MET cc_start: 0.8020 (ttm) cc_final: 0.7750 (mtp) REVERT: E 117 ASP cc_start: 0.7866 (m-30) cc_final: 0.7635 (m-30) REVERT: E 140 LYS cc_start: 0.8285 (ptpt) cc_final: 0.7963 (mtpt) outliers start: 23 outliers final: 17 residues processed: 169 average time/residue: 0.2457 time to fit residues: 58.4634 Evaluate side-chains 171 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10619 Z= 0.193 Angle : 0.514 6.916 14348 Z= 0.261 Chirality : 0.041 0.166 1682 Planarity : 0.004 0.038 1804 Dihedral : 4.394 20.759 1402 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.17 % Allowed : 13.63 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1343 helix: 0.48 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : 0.61 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 35 HIS 0.004 0.001 HIS D 52 PHE 0.018 0.001 PHE B 149 TYR 0.016 0.002 TYR D 197 ARG 0.009 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.075 Fit side-chains REVERT: B 113 MET cc_start: 0.7412 (ptm) cc_final: 0.6928 (ptt) REVERT: B 140 LYS cc_start: 0.8043 (ttmp) cc_final: 0.7529 (mtmm) REVERT: D 33 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8362 (tp) REVERT: D 151 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7097 (mt-10) REVERT: E 64 LYS cc_start: 0.7784 (pttm) cc_final: 0.6608 (mmmt) REVERT: E 104 GLU cc_start: 0.7686 (mp0) cc_final: 0.7318 (mm-30) REVERT: E 113 MET cc_start: 0.8007 (ttm) cc_final: 0.7760 (mtp) REVERT: E 117 ASP cc_start: 0.7897 (m-30) cc_final: 0.7664 (m-30) REVERT: E 140 LYS cc_start: 0.8306 (ptpt) cc_final: 0.7968 (mtpt) REVERT: E 207 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8299 (tt) outliers start: 24 outliers final: 20 residues processed: 177 average time/residue: 0.2470 time to fit residues: 61.4725 Evaluate side-chains 175 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 78 optimal weight: 0.0970 chunk 126 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10619 Z= 0.156 Angle : 0.488 6.256 14348 Z= 0.249 Chirality : 0.040 0.145 1682 Planarity : 0.004 0.037 1804 Dihedral : 4.277 20.422 1402 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.17 % Allowed : 14.08 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1343 helix: 0.64 (0.16), residues: 1098 sheet: None (None), residues: 0 loop : 0.50 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 203 HIS 0.003 0.001 HIS B 52 PHE 0.015 0.001 PHE B 149 TYR 0.015 0.002 TYR D 197 ARG 0.008 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.132 Fit side-chains REVERT: B 113 MET cc_start: 0.7227 (ptm) cc_final: 0.6772 (ptt) REVERT: B 140 LYS cc_start: 0.8019 (ttmp) cc_final: 0.7523 (mtmm) REVERT: C 106 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7175 (tp30) REVERT: C 171 LEU cc_start: 0.6799 (mp) cc_final: 0.6531 (mp) REVERT: D 33 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8279 (tp) REVERT: D 151 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7088 (mt-10) REVERT: E 64 LYS cc_start: 0.7765 (pttm) cc_final: 0.6603 (mmmt) REVERT: E 104 GLU cc_start: 0.7648 (mp0) cc_final: 0.7288 (mm-30) REVERT: E 117 ASP cc_start: 0.7792 (m-30) cc_final: 0.7545 (m-30) REVERT: E 140 LYS cc_start: 0.8274 (ptpt) cc_final: 0.7999 (mtpt) REVERT: E 207 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8323 (tt) outliers start: 24 outliers final: 18 residues processed: 181 average time/residue: 0.2295 time to fit residues: 58.4999 Evaluate side-chains 176 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 112 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10619 Z= 0.239 Angle : 0.535 7.318 14348 Z= 0.270 Chirality : 0.042 0.147 1682 Planarity : 0.004 0.037 1804 Dihedral : 4.413 20.822 1402 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.81 % Allowed : 14.35 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1343 helix: 0.59 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : 0.68 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 16 HIS 0.004 0.001 HIS D 52 PHE 0.020 0.002 PHE B 149 TYR 0.019 0.002 TYR D 197 ARG 0.009 0.000 ARG C 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.154 Fit side-chains REVERT: B 113 MET cc_start: 0.7319 (ptm) cc_final: 0.6781 (ptt) REVERT: B 140 LYS cc_start: 0.8048 (ttmp) cc_final: 0.7498 (mtmm) REVERT: C 212 MET cc_start: 0.8273 (mmp) cc_final: 0.8017 (mmp) REVERT: D 33 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8380 (tp) REVERT: D 151 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7107 (mt-10) REVERT: E 64 LYS cc_start: 0.7776 (pttm) cc_final: 0.6591 (mmmt) REVERT: E 104 GLU cc_start: 0.7671 (mp0) cc_final: 0.7328 (mm-30) REVERT: E 140 LYS cc_start: 0.8329 (ptpt) cc_final: 0.8008 (mtpt) REVERT: E 207 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8303 (tt) outliers start: 20 outliers final: 17 residues processed: 177 average time/residue: 0.2318 time to fit residues: 57.9216 Evaluate side-chains 177 residues out of total 1108 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 13 optimal weight: 0.0030 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS D 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.142052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.111481 restraints weight = 11399.478| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.57 r_work: 0.2997 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10619 Z= 0.160 Angle : 0.503 7.689 14348 Z= 0.252 Chirality : 0.040 0.130 1682 Planarity : 0.004 0.039 1804 Dihedral : 4.276 20.522 1402 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.90 % Allowed : 14.53 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1343 helix: 0.78 (0.16), residues: 1086 sheet: None (None), residues: 0 loop : 0.67 (0.43), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 203 HIS 0.003 0.001 HIS B 52 PHE 0.013 0.001 PHE D 149 TYR 0.016 0.002 TYR D 197 ARG 0.009 0.000 ARG C 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.97 seconds wall clock time: 44 minutes 9.81 seconds (2649.81 seconds total)