Starting phenix.real_space_refine on Thu Sep 26 01:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/09_2024/6k1h_9906.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/09_2024/6k1h_9906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/09_2024/6k1h_9906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/09_2024/6k1h_9906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/09_2024/6k1h_9906.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/09_2024/6k1h_9906.cif" } resolution = 3.52 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= 0.001 sd= 0.015 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 75 5.16 5 C 7704 2.51 5 N 1956 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11769 Number of models: 1 Model: "" Number of chains: 9 Chain: "Z" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2105 Classifications: {'peptide': 273} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 258} Chain: "Y" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1806 Classifications: {'peptide': 247} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 238} Chain: "F" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2105 Classifications: {'peptide': 273} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 258} Chain: "E" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1806 Classifications: {'peptide': 247} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 238} Chain: "C" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2105 Classifications: {'peptide': 273} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 258} Chain: "B" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1806 Classifications: {'peptide': 247} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 238} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.40, per 1000 atoms: 0.63 Number of scatterers: 11769 At special positions: 0 Unit cell: (128.448, 123.096, 94.998, 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 75 16.00 O 2034 8.00 N 1956 7.00 C 7704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.9 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2790 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 71.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'Z' and resid 17 through 29 removed outlier: 3.628A pdb=" N ILE Z 21 " --> pdb=" O THR Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 57 Proline residue: Z 51 - end of helix removed outlier: 3.875A pdb=" N ARG Z 55 " --> pdb=" O PRO Z 51 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR Z 57 " --> pdb=" O ILE Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 65 through 71 removed outlier: 3.517A pdb=" N ARG Z 69 " --> pdb=" O LYS Z 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 98 removed outlier: 3.529A pdb=" N GLU Z 93 " --> pdb=" O THR Z 89 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU Z 94 " --> pdb=" O LEU Z 90 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN Z 95 " --> pdb=" O ALA Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 127 removed outlier: 4.341A pdb=" N ASN Z 108 " --> pdb=" O ASP Z 104 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY Z 116 " --> pdb=" O VAL Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix removed outlier: 3.702A pdb=" N ASP Z 123 " --> pdb=" O ALA Z 119 " (cutoff:3.500A) Proline residue: Z 124 - end of helix Processing helix chain 'Z' and resid 130 through 138 Processing helix chain 'Z' and resid 151 through 161 removed outlier: 3.537A pdb=" N ASN Z 158 " --> pdb=" O PHE Z 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 174 removed outlier: 3.623A pdb=" N TYR Z 171 " --> pdb=" O TYR Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 176 through 178 No H-bonds generated for 'chain 'Z' and resid 176 through 178' Processing helix chain 'Z' and resid 179 through 184 removed outlier: 3.997A pdb=" N MET Z 183 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 210 removed outlier: 3.648A pdb=" N SER Z 196 " --> pdb=" O THR Z 192 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE Z 197 " --> pdb=" O GLU Z 193 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU Z 200 " --> pdb=" O SER Z 196 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 242 removed outlier: 3.703A pdb=" N ILE Z 237 " --> pdb=" O THR Z 233 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU Z 241 " --> pdb=" O ILE Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 244 through 258 Processing helix chain 'Z' and resid 259 through 261 No H-bonds generated for 'chain 'Z' and resid 259 through 261' Processing helix chain 'Z' and resid 263 through 266 Processing helix chain 'Z' and resid 267 through 278 removed outlier: 3.514A pdb=" N ILE Z 276 " --> pdb=" O PHE Z 272 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.608A pdb=" N VAL Y 9 " --> pdb=" O THR Y 5 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER Y 22 " --> pdb=" O ALA Y 18 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 44 removed outlier: 3.737A pdb=" N VAL Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL Y 42 " --> pdb=" O LEU Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 61 removed outlier: 4.070A pdb=" N ILE Y 52 " --> pdb=" O THR Y 48 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 87 removed outlier: 4.383A pdb=" N VAL Y 85 " --> pdb=" O SER Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 91 through 117 removed outlier: 4.134A pdb=" N ILE Y 100 " --> pdb=" O ILE Y 96 " (cutoff:3.500A) Proline residue: Y 101 - end of helix removed outlier: 3.616A pdb=" N GLN Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL Y 108 " --> pdb=" O ALA Y 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 121 Processing helix chain 'Y' and resid 124 through 129 Processing helix chain 'Y' and resid 133 through 141 removed outlier: 3.780A pdb=" N ILE Y 139 " --> pdb=" O ALA Y 135 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL Y 141 " --> pdb=" O SER Y 137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 151 removed outlier: 3.926A pdb=" N VAL Y 151 " --> pdb=" O ALA Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 158 removed outlier: 3.733A pdb=" N VAL Y 158 " --> pdb=" O PRO Y 154 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 175 through 186 removed outlier: 3.705A pdb=" N ILE Y 184 " --> pdb=" O ASN Y 180 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA Y 185 " --> pdb=" O GLY Y 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 201 removed outlier: 3.889A pdb=" N GLY Y 193 " --> pdb=" O ILE Y 189 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL Y 197 " --> pdb=" O GLY Y 193 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET Y 200 " --> pdb=" O MET Y 196 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 219 removed outlier: 3.721A pdb=" N ALA Y 217 " --> pdb=" O GLY Y 213 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 241 removed outlier: 3.541A pdb=" N THR Y 232 " --> pdb=" O GLY Y 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 242 through 246 Processing helix chain 'F' and resid 17 through 29 removed outlier: 3.627A pdb=" N ILE F 21 " --> pdb=" O THR F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 57 Proline residue: F 51 - end of helix removed outlier: 3.875A pdb=" N ARG F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR F 57 " --> pdb=" O ILE F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 71 removed outlier: 3.518A pdb=" N ARG F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 98 removed outlier: 3.529A pdb=" N GLU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 127 removed outlier: 4.340A pdb=" N ASN F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Proline residue: F 117 - end of helix removed outlier: 3.701A pdb=" N ASP F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 130 through 138 Processing helix chain 'F' and resid 151 through 161 removed outlier: 3.537A pdb=" N ASN F 158 " --> pdb=" O PHE F 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.623A pdb=" N TYR F 171 " --> pdb=" O TYR F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 179 through 184 removed outlier: 3.997A pdb=" N MET F 183 " --> pdb=" O ILE F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 210 removed outlier: 3.648A pdb=" N SER F 196 " --> pdb=" O THR F 192 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 242 removed outlier: 3.703A pdb=" N ILE F 237 " --> pdb=" O THR F 233 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 241 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 263 through 266 Processing helix chain 'F' and resid 267 through 278 removed outlier: 3.514A pdb=" N ILE F 276 " --> pdb=" O PHE F 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 removed outlier: 3.607A pdb=" N VAL E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU E 10 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 44 removed outlier: 3.736A pdb=" N VAL E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 61 removed outlier: 4.072A pdb=" N ILE E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 removed outlier: 4.383A pdb=" N VAL E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 117 removed outlier: 4.134A pdb=" N ILE E 100 " --> pdb=" O ILE E 96 " (cutoff:3.500A) Proline residue: E 101 - end of helix removed outlier: 3.616A pdb=" N GLN E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.780A pdb=" N ILE E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.926A pdb=" N VAL E 151 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 3.733A pdb=" N VAL E 158 " --> pdb=" O PRO E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 175 through 186 removed outlier: 3.704A pdb=" N ILE E 184 " --> pdb=" O ASN E 180 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA E 185 " --> pdb=" O GLY E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.889A pdb=" N GLY E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET E 200 " --> pdb=" O MET E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 219 removed outlier: 3.722A pdb=" N ALA E 217 " --> pdb=" O GLY E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 241 removed outlier: 3.541A pdb=" N THR E 232 " --> pdb=" O GLY E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 246 Processing helix chain 'C' and resid 17 through 29 removed outlier: 3.627A pdb=" N ILE C 21 " --> pdb=" O THR C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 57 Proline residue: C 51 - end of helix removed outlier: 3.874A pdb=" N ARG C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 removed outlier: 3.517A pdb=" N ARG C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 98 removed outlier: 3.529A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 127 removed outlier: 4.340A pdb=" N ASN C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Proline residue: C 117 - end of helix removed outlier: 3.702A pdb=" N ASP C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.537A pdb=" N ASN C 158 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.623A pdb=" N TYR C 171 " --> pdb=" O TYR C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 178 No H-bonds generated for 'chain 'C' and resid 176 through 178' Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.997A pdb=" N MET C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 210 removed outlier: 3.648A pdb=" N SER C 196 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.703A pdb=" N ILE C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 263 through 266 Processing helix chain 'C' and resid 267 through 278 removed outlier: 3.514A pdb=" N ILE C 276 " --> pdb=" O PHE C 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.608A pdb=" N VAL B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 removed outlier: 3.736A pdb=" N VAL B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 61 removed outlier: 4.070A pdb=" N ILE B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 removed outlier: 4.383A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 117 removed outlier: 4.134A pdb=" N ILE B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Proline residue: B 101 - end of helix removed outlier: 3.616A pdb=" N GLN B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.780A pdb=" N ILE B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.926A pdb=" N VAL B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.733A pdb=" N VAL B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.705A pdb=" N ILE B 184 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 201 removed outlier: 3.889A pdb=" N GLY B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 219 removed outlier: 3.721A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 removed outlier: 3.541A pdb=" N THR B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 582 hydrogen bonds defined for protein. 1701 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: 3.00 Time building geometry restraints manager: 3.35 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: 2814 1.33 - 1.45: 2231 1.45 - 1.57: 6817 1.57 - 1.69: 3 1.69 - 1.81: 135 Bond restraints: 12000 Sorted by residual: bond pdb=" N GLN F 32 " pdb=" CA GLN F 32 " ideal model delta sigma weight residual 1.456 1.514 -0.057 1.27e-02 6.20e+03 2.05e+01 bond pdb=" N GLN C 32 " pdb=" CA GLN C 32 " ideal model delta sigma weight residual 1.456 1.511 -0.054 1.27e-02 6.20e+03 1.83e+01 bond pdb=" N GLN Z 32 " pdb=" CA GLN Z 32 " ideal model delta sigma weight residual 1.456 1.510 -0.054 1.27e-02 6.20e+03 1.83e+01 bond pdb=" CA GLN F 32 " pdb=" C GLN F 32 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.23e-02 6.61e+03 1.33e+01 bond pdb=" CA GLN C 32 " pdb=" C GLN C 32 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.23e-02 6.61e+03 1.26e+01 ... (remaining 11995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 16055 3.18 - 6.36: 235 6.36 - 9.53: 23 9.53 - 12.71: 6 12.71 - 15.89: 1 Bond angle restraints: 16320 Sorted by residual: angle pdb=" N ARG Y 247 " pdb=" CA ARG Y 247 " pdb=" C ARG Y 247 " ideal model delta sigma weight residual 109.18 125.07 -15.89 1.42e+00 4.96e-01 1.25e+02 angle pdb=" CA GLN C 32 " pdb=" C GLN C 32 " pdb=" O GLN C 32 " ideal model delta sigma weight residual 121.15 112.44 8.71 1.10e+00 8.26e-01 6.27e+01 angle pdb=" CA GLN Z 32 " pdb=" C GLN Z 32 " pdb=" O GLN Z 32 " ideal model delta sigma weight residual 121.15 112.70 8.45 1.10e+00 8.26e-01 5.90e+01 angle pdb=" CA GLN F 32 " pdb=" C GLN F 32 " pdb=" O GLN F 32 " ideal model delta sigma weight residual 121.15 112.79 8.36 1.10e+00 8.26e-01 5.77e+01 angle pdb=" N ARG B 247 " pdb=" CA ARG B 247 " pdb=" C ARG B 247 " ideal model delta sigma weight residual 108.86 118.13 -9.27 1.41e+00 5.03e-01 4.32e+01 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.58: 6560 20.58 - 41.15: 401 41.15 - 61.73: 52 61.73 - 82.31: 28 82.31 - 102.89: 12 Dihedral angle restraints: 7053 sinusoidal: 2676 harmonic: 4377 Sorted by residual: dihedral pdb=" CA ARG C 221 " pdb=" C ARG C 221 " pdb=" N ILE C 222 " pdb=" CA ILE C 222 " ideal model delta harmonic sigma weight residual -180.00 -139.25 -40.75 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA ARG Z 221 " pdb=" C ARG Z 221 " pdb=" N ILE Z 222 " pdb=" CA ILE Z 222 " ideal model delta harmonic sigma weight residual -180.00 -139.27 -40.73 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA ARG F 221 " pdb=" C ARG F 221 " pdb=" N ILE F 222 " pdb=" CA ILE F 222 " ideal model delta harmonic sigma weight residual -180.00 -139.29 -40.71 0 5.00e+00 4.00e-02 6.63e+01 ... (remaining 7050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1648 0.067 - 0.134: 320 0.134 - 0.200: 15 0.200 - 0.267: 1 0.267 - 0.334: 2 Chirality restraints: 1986 Sorted by residual: chirality pdb=" CA ARG Y 247 " pdb=" N ARG Y 247 " pdb=" C ARG Y 247 " pdb=" CB ARG Y 247 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ARG E 247 " pdb=" N ARG E 247 " pdb=" C ARG E 247 " pdb=" CB ARG E 247 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ARG B 247 " pdb=" N ARG B 247 " pdb=" C ARG B 247 " pdb=" CB ARG B 247 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1983 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 32 " -0.022 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C GLN F 32 " 0.082 2.00e-02 2.50e+03 pdb=" O GLN F 32 " -0.031 2.00e-02 2.50e+03 pdb=" N GLY F 33 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 32 " 0.022 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C GLN C 32 " -0.081 2.00e-02 2.50e+03 pdb=" O GLN C 32 " 0.031 2.00e-02 2.50e+03 pdb=" N GLY C 33 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN Z 32 " 0.022 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C GLN Z 32 " -0.080 2.00e-02 2.50e+03 pdb=" O GLN Z 32 " 0.030 2.00e-02 2.50e+03 pdb=" N GLY Z 33 " 0.028 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 39 2.40 - 3.02: 7235 3.02 - 3.65: 17525 3.65 - 4.27: 26919 4.27 - 4.90: 43597 Nonbonded interactions: 95315 Sorted by model distance: nonbonded pdb=" CZ PHE Y 219 " pdb=" ND2 ASN B 223 " model vdw 1.774 3.420 nonbonded pdb=" ND2 ASN Y 223 " pdb=" CZ PHE E 219 " model vdw 1.774 3.420 nonbonded pdb=" ND2 ASN E 223 " pdb=" CZ PHE B 219 " model vdw 1.775 3.420 nonbonded pdb=" OE1 GLU Z 193 " pdb=" OH TYR Y 245 " model vdw 2.032 3.040 nonbonded pdb=" OE1 GLU C 193 " pdb=" OH TYR B 245 " model vdw 2.032 3.040 ... (remaining 95310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'Y' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'Z' } 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 28.550 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.007 0.071 12000 Z= 0.427 Angle : 0.975 15.892 16320 Z= 0.575 Chirality : 0.050 0.334 1986 Planarity : 0.007 0.061 2028 Dihedral : 15.198 102.886 4263 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.31 % Favored : 86.50 % Rotamer: Outliers : 0.90 % Allowed : 0.49 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -4.44 (0.18), residues: 1548 helix: -2.52 (0.14), residues: 1101 sheet: None (None), residues: 0 loop : -3.61 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 138 HIS 0.005 0.001 HIS Z 71 PHE 0.017 0.002 PHE B 222 TYR 0.011 0.001 TYR C 171 ARG 0.009 0.001 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 272 time to evaluate : 1.253 Fit side-chains REVERT: Z 129 THR cc_start: 0.8711 (p) cc_final: 0.8485 (p) REVERT: Y 52 ILE cc_start: 0.8815 (mt) cc_final: 0.8593 (mt) REVERT: Y 149 MET cc_start: 0.7222 (mmt) cc_final: 0.6972 (tmm) REVERT: F 71 HIS cc_start: 0.6698 (m-70) cc_final: 0.6460 (m-70) REVERT: F 156 LEU cc_start: 0.9442 (mm) cc_final: 0.9195 (mt) REVERT: F 190 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7298 (mttt) REVERT: E 16 CYS cc_start: 0.7870 (t) cc_final: 0.7573 (t) REVERT: E 149 MET cc_start: 0.6964 (mmt) cc_final: 0.6698 (tmm) REVERT: E 234 MET cc_start: 0.7998 (mtp) cc_final: 0.7594 (mtm) REVERT: C 14 LYS cc_start: 0.7204 (mmmt) cc_final: 0.6976 (mmmt) REVERT: C 71 HIS cc_start: 0.7069 (m-70) cc_final: 0.6788 (m-70) REVERT: C 143 MET cc_start: 0.8604 (mmt) cc_final: 0.8360 (mmt) REVERT: C 159 LEU cc_start: 0.8801 (mt) cc_final: 0.8447 (mt) REVERT: C 190 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7238 (mttt) REVERT: B 180 ASN cc_start: 0.8669 (m-40) cc_final: 0.7931 (m-40) outliers start: 11 outliers final: 8 residues processed: 282 average time/residue: 0.2181 time to fit residues: 89.6415 Evaluate side-chains 222 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 214 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain Y residue 248 VAL Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 0.0670 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 ASN ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 240 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12000 Z= 0.324 Angle : 0.796 10.312 16320 Z= 0.416 Chirality : 0.047 0.183 1986 Planarity : 0.007 0.062 2028 Dihedral : 8.461 54.847 1733 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.27 % Favored : 89.53 % Rotamer: Outliers : 2.53 % Allowed : 11.60 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -3.85 (0.18), residues: 1548 helix: -1.91 (0.14), residues: 1110 sheet: None (None), residues: 0 loop : -3.92 (0.22), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 35 HIS 0.005 0.002 HIS C 230 PHE 0.023 0.002 PHE C 25 TYR 0.016 0.002 TYR E 194 ARG 0.004 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 236 time to evaluate : 1.855 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9201 (mm) cc_final: 0.8965 (mt) REVERT: Y 52 ILE cc_start: 0.8803 (mt) cc_final: 0.8597 (mt) REVERT: Y 149 MET cc_start: 0.7440 (mmt) cc_final: 0.6977 (tmm) REVERT: Y 150 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7329 (tmm160) REVERT: Y 180 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8285 (m-40) REVERT: Y 184 ILE cc_start: 0.8608 (mt) cc_final: 0.8312 (mp) REVERT: F 156 LEU cc_start: 0.9256 (mm) cc_final: 0.9008 (mt) REVERT: F 190 LYS cc_start: 0.7887 (mtpt) cc_final: 0.6922 (mttt) REVERT: F 209 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7937 (ttmt) REVERT: E 51 ILE cc_start: 0.8999 (mt) cc_final: 0.8717 (mp) REVERT: E 149 MET cc_start: 0.7209 (mmt) cc_final: 0.6627 (tmm) REVERT: E 150 ARG cc_start: 0.7376 (mtt180) cc_final: 0.6933 (tmm160) REVERT: E 170 MET cc_start: 0.6866 (tpt) cc_final: 0.6539 (tpt) REVERT: E 234 MET cc_start: 0.7947 (mtp) cc_final: 0.7585 (mtm) REVERT: C 143 MET cc_start: 0.8678 (mmt) cc_final: 0.8435 (mmt) REVERT: C 190 LYS cc_start: 0.7873 (mtpt) cc_final: 0.6920 (mttt) REVERT: B 64 MET cc_start: 0.8515 (pmm) cc_final: 0.7610 (pmm) REVERT: B 180 ASN cc_start: 0.8614 (m-40) cc_final: 0.8010 (m-40) REVERT: B 223 ASN cc_start: 0.8155 (m-40) cc_final: 0.7917 (m-40) outliers start: 31 outliers final: 25 residues processed: 249 average time/residue: 0.2405 time to fit residues: 87.3622 Evaluate side-chains 229 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 180 ASN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain Y residue 248 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 71 HIS ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12000 Z= 0.282 Angle : 0.719 10.270 16320 Z= 0.379 Chirality : 0.045 0.173 1986 Planarity : 0.006 0.061 2028 Dihedral : 6.712 49.934 1726 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.34 % Favored : 89.47 % Rotamer: Outliers : 3.84 % Allowed : 14.38 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -3.39 (0.19), residues: 1548 helix: -1.53 (0.14), residues: 1140 sheet: None (None), residues: 0 loop : -4.00 (0.23), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 210 HIS 0.004 0.001 HIS C 71 PHE 0.022 0.002 PHE E 12 TYR 0.029 0.002 TYR F 57 ARG 0.005 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 224 time to evaluate : 1.545 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9194 (mm) cc_final: 0.8910 (mt) REVERT: Y 149 MET cc_start: 0.7424 (mmt) cc_final: 0.6948 (tmm) REVERT: Y 150 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7248 (tmm160) REVERT: Y 180 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8169 (m-40) REVERT: Y 184 ILE cc_start: 0.8571 (mt) cc_final: 0.8253 (mp) REVERT: F 156 LEU cc_start: 0.9226 (mm) cc_final: 0.8905 (mt) REVERT: F 190 LYS cc_start: 0.7831 (mtpt) cc_final: 0.6889 (mttt) REVERT: F 209 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8106 (ttmt) REVERT: E 64 MET cc_start: 0.8568 (pmm) cc_final: 0.8283 (pmm) REVERT: E 149 MET cc_start: 0.7131 (mmt) cc_final: 0.6636 (tmm) REVERT: E 150 ARG cc_start: 0.7683 (mtt180) cc_final: 0.6953 (tmm160) REVERT: E 234 MET cc_start: 0.7858 (mtp) cc_final: 0.7526 (mtm) REVERT: C 14 LYS cc_start: 0.7459 (mmmt) cc_final: 0.6023 (mmmt) REVERT: C 92 LEU cc_start: 0.9112 (mm) cc_final: 0.8849 (mp) REVERT: C 190 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7184 (mttt) REVERT: B 64 MET cc_start: 0.8566 (pmm) cc_final: 0.7953 (pmm) REVERT: B 180 ASN cc_start: 0.8641 (m-40) cc_final: 0.8004 (m-40) REVERT: B 220 THR cc_start: 0.8860 (m) cc_final: 0.8593 (p) REVERT: B 223 ASN cc_start: 0.7813 (m-40) cc_final: 0.7531 (m110) outliers start: 47 outliers final: 33 residues processed: 245 average time/residue: 0.2265 time to fit residues: 81.0703 Evaluate side-chains 242 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 180 ASN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 180 ASN Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 0.3980 chunk 147 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12000 Z= 0.275 Angle : 0.703 10.405 16320 Z= 0.368 Chirality : 0.045 0.178 1986 Planarity : 0.006 0.061 2028 Dihedral : 6.511 49.103 1725 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.14 % Favored : 89.66 % Rotamer: Outliers : 4.90 % Allowed : 15.28 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -3.05 (0.20), residues: 1548 helix: -1.29 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -3.88 (0.23), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 210 HIS 0.004 0.001 HIS B 140 PHE 0.024 0.002 PHE Y 12 TYR 0.014 0.001 TYR F 57 ARG 0.004 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 225 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: Z 156 LEU cc_start: 0.9148 (mm) cc_final: 0.8853 (mt) REVERT: Y 149 MET cc_start: 0.7665 (mmt) cc_final: 0.7137 (tmm) REVERT: Y 150 ARG cc_start: 0.7755 (mtt180) cc_final: 0.7274 (tmm160) REVERT: F 156 LEU cc_start: 0.9231 (mm) cc_final: 0.8910 (mt) REVERT: F 190 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7200 (mttt) REVERT: E 28 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8654 (mm-40) REVERT: E 51 ILE cc_start: 0.8879 (mt) cc_final: 0.8600 (mp) REVERT: E 150 ARG cc_start: 0.7677 (mtt180) cc_final: 0.6910 (tmm160) REVERT: E 234 MET cc_start: 0.7862 (mtp) cc_final: 0.7552 (mtm) REVERT: C 92 LEU cc_start: 0.9147 (mm) cc_final: 0.8902 (mp) REVERT: C 190 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7166 (mttt) REVERT: B 64 MET cc_start: 0.8611 (pmm) cc_final: 0.8139 (pmm) REVERT: B 168 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7034 (mm-40) REVERT: B 180 ASN cc_start: 0.8596 (m-40) cc_final: 0.7958 (m-40) REVERT: B 220 THR cc_start: 0.8844 (m) cc_final: 0.8628 (p) outliers start: 60 outliers final: 47 residues processed: 257 average time/residue: 0.2274 time to fit residues: 84.6618 Evaluate side-chains 255 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 208 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 223 ASN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 0.0470 chunk 61 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 90 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12000 Z= 0.285 Angle : 0.691 10.217 16320 Z= 0.365 Chirality : 0.045 0.176 1986 Planarity : 0.006 0.061 2028 Dihedral : 6.329 47.758 1725 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.59 % Favored : 89.21 % Rotamer: Outliers : 6.13 % Allowed : 15.60 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -2.87 (0.20), residues: 1548 helix: -1.17 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -3.75 (0.24), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 210 HIS 0.004 0.001 HIS Y 140 PHE 0.023 0.002 PHE B 12 TYR 0.009 0.001 TYR F 57 ARG 0.003 0.001 ARG F 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 228 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: Z 156 LEU cc_start: 0.9167 (mm) cc_final: 0.8859 (mt) REVERT: Y 20 MET cc_start: 0.7706 (mmm) cc_final: 0.7481 (mmm) REVERT: Y 149 MET cc_start: 0.7630 (mmt) cc_final: 0.7098 (tmm) REVERT: Y 150 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7272 (tmm160) REVERT: F 156 LEU cc_start: 0.9240 (mm) cc_final: 0.8918 (mt) REVERT: F 190 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7207 (mttt) REVERT: E 28 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8714 (mm-40) REVERT: E 150 ARG cc_start: 0.7687 (mtt180) cc_final: 0.6913 (tmm160) REVERT: E 172 ASN cc_start: 0.7868 (m110) cc_final: 0.7640 (p0) REVERT: E 234 MET cc_start: 0.7895 (mtp) cc_final: 0.7609 (mtm) REVERT: C 190 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7115 (mttt) REVERT: B 168 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7105 (mm-40) REVERT: B 180 ASN cc_start: 0.8601 (m-40) cc_final: 0.7980 (m-40) REVERT: B 220 THR cc_start: 0.8860 (m) cc_final: 0.8631 (p) outliers start: 75 outliers final: 55 residues processed: 276 average time/residue: 0.2139 time to fit residues: 86.3433 Evaluate side-chains 264 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 209 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 223 ASN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12000 Z= 0.236 Angle : 0.676 11.201 16320 Z= 0.354 Chirality : 0.044 0.169 1986 Planarity : 0.005 0.059 2028 Dihedral : 6.196 47.665 1725 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.43 % Favored : 90.37 % Rotamer: Outliers : 5.23 % Allowed : 16.83 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -2.58 (0.20), residues: 1548 helix: -0.95 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -3.60 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 210 HIS 0.005 0.001 HIS Y 140 PHE 0.023 0.001 PHE B 12 TYR 0.009 0.001 TYR C 171 ARG 0.003 0.000 ARG Z 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 223 time to evaluate : 1.315 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9091 (mm) cc_final: 0.8793 (mt) REVERT: Y 149 MET cc_start: 0.7649 (mmt) cc_final: 0.6918 (tmm) REVERT: Y 150 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7229 (tmm160) REVERT: Y 172 ASN cc_start: 0.7805 (m110) cc_final: 0.7426 (p0) REVERT: F 190 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7192 (mttt) REVERT: F 198 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8289 (tp) REVERT: E 150 ARG cc_start: 0.7614 (mtt180) cc_final: 0.6836 (tmm160) REVERT: E 172 ASN cc_start: 0.7879 (m110) cc_final: 0.7614 (p0) REVERT: E 234 MET cc_start: 0.7856 (mtp) cc_final: 0.7546 (mtm) REVERT: C 57 TYR cc_start: 0.8522 (m-10) cc_final: 0.8231 (m-10) REVERT: C 190 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7086 (mttt) REVERT: B 180 ASN cc_start: 0.8525 (m-40) cc_final: 0.7915 (m-40) REVERT: B 220 THR cc_start: 0.8800 (m) cc_final: 0.8569 (p) outliers start: 64 outliers final: 50 residues processed: 262 average time/residue: 0.1805 time to fit residues: 69.9757 Evaluate side-chains 258 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 207 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.0670 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 92 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12000 Z= 0.204 Angle : 0.663 10.448 16320 Z= 0.348 Chirality : 0.043 0.162 1986 Planarity : 0.005 0.057 2028 Dihedral : 5.989 48.233 1725 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.91 % Favored : 91.02 % Rotamer: Outliers : 4.98 % Allowed : 17.16 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.32 (0.21), residues: 1548 helix: -0.75 (0.16), residues: 1122 sheet: None (None), residues: 0 loop : -3.50 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 127 HIS 0.006 0.001 HIS Y 140 PHE 0.025 0.001 PHE Z 25 TYR 0.008 0.001 TYR F 57 ARG 0.003 0.000 ARG Z 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 230 time to evaluate : 1.255 Fit side-chains REVERT: Z 57 TYR cc_start: 0.8452 (m-80) cc_final: 0.8210 (m-10) REVERT: Z 156 LEU cc_start: 0.9091 (mm) cc_final: 0.8778 (mt) REVERT: Y 149 MET cc_start: 0.7662 (mmt) cc_final: 0.6850 (tmm) REVERT: Y 150 ARG cc_start: 0.7531 (mtt180) cc_final: 0.7134 (tmm160) REVERT: Y 172 ASN cc_start: 0.7767 (m110) cc_final: 0.7517 (p0) REVERT: Y 180 ASN cc_start: 0.8201 (m-40) cc_final: 0.7771 (m-40) REVERT: F 57 TYR cc_start: 0.8061 (m-10) cc_final: 0.7759 (m-10) REVERT: F 190 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7145 (mttt) REVERT: F 198 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8114 (tp) REVERT: E 150 ARG cc_start: 0.7479 (mtt180) cc_final: 0.6775 (tmm160) REVERT: E 172 ASN cc_start: 0.7844 (m110) cc_final: 0.7561 (p0) REVERT: E 234 MET cc_start: 0.7832 (mtp) cc_final: 0.7544 (mtm) REVERT: C 57 TYR cc_start: 0.8469 (m-10) cc_final: 0.8076 (m-10) REVERT: C 66 GLN cc_start: 0.6178 (tt0) cc_final: 0.5922 (tp40) REVERT: C 190 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7045 (mttt) REVERT: C 221 ARG cc_start: 0.3519 (OUTLIER) cc_final: 0.2479 (ttm170) REVERT: B 180 ASN cc_start: 0.8568 (m-40) cc_final: 0.7997 (m-40) REVERT: B 220 THR cc_start: 0.8746 (m) cc_final: 0.8506 (p) outliers start: 61 outliers final: 41 residues processed: 268 average time/residue: 0.2136 time to fit residues: 83.5718 Evaluate side-chains 258 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 247 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 134 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12000 Z= 0.215 Angle : 0.668 10.496 16320 Z= 0.349 Chirality : 0.043 0.167 1986 Planarity : 0.005 0.055 2028 Dihedral : 5.881 48.810 1724 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 5.15 % Allowed : 17.24 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -2.19 (0.21), residues: 1548 helix: -0.68 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -3.41 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 127 HIS 0.008 0.001 HIS B 140 PHE 0.025 0.001 PHE E 12 TYR 0.007 0.001 TYR C 171 ARG 0.009 0.000 ARG F 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 232 time to evaluate : 1.304 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9141 (mm) cc_final: 0.8832 (mt) REVERT: Y 28 GLN cc_start: 0.8803 (mm110) cc_final: 0.8589 (mm-40) REVERT: Y 149 MET cc_start: 0.7640 (mmt) cc_final: 0.6807 (tmm) REVERT: Y 150 ARG cc_start: 0.7512 (mtt180) cc_final: 0.6962 (tmm160) REVERT: Y 180 ASN cc_start: 0.8193 (m-40) cc_final: 0.7801 (m-40) REVERT: F 190 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7136 (mttt) REVERT: F 198 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8259 (tp) REVERT: E 28 GLN cc_start: 0.8798 (mm110) cc_final: 0.8445 (mm110) REVERT: E 149 MET cc_start: 0.7086 (mmt) cc_final: 0.6526 (mmt) REVERT: E 150 ARG cc_start: 0.7419 (mtt180) cc_final: 0.6722 (tmm160) REVERT: E 172 ASN cc_start: 0.7869 (m110) cc_final: 0.7586 (p0) REVERT: E 234 MET cc_start: 0.7819 (mtp) cc_final: 0.7529 (mtm) REVERT: C 57 TYR cc_start: 0.8441 (m-10) cc_final: 0.8008 (m-10) REVERT: C 66 GLN cc_start: 0.6180 (tt0) cc_final: 0.5867 (tp40) REVERT: C 190 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7034 (mttt) REVERT: B 116 ILE cc_start: 0.8650 (tp) cc_final: 0.8342 (tp) REVERT: B 180 ASN cc_start: 0.8504 (m-40) cc_final: 0.7961 (m-40) REVERT: B 220 THR cc_start: 0.8633 (m) cc_final: 0.8430 (p) outliers start: 63 outliers final: 52 residues processed: 272 average time/residue: 0.2053 time to fit residues: 82.3939 Evaluate side-chains 271 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 218 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 198 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 247 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 0.0470 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12000 Z= 0.214 Angle : 0.688 15.947 16320 Z= 0.355 Chirality : 0.044 0.177 1986 Planarity : 0.005 0.055 2028 Dihedral : 5.805 49.012 1724 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 4.49 % Allowed : 18.22 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 (0.21), residues: 1548 helix: -0.59 (0.16), residues: 1137 sheet: None (None), residues: 0 loop : -3.51 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 210 HIS 0.006 0.001 HIS B 140 PHE 0.024 0.001 PHE E 12 TYR 0.011 0.001 TYR F 57 ARG 0.008 0.001 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 223 time to evaluate : 1.398 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9126 (mm) cc_final: 0.8808 (mt) REVERT: Z 266 TRP cc_start: 0.7901 (m100) cc_final: 0.7348 (m-10) REVERT: Y 149 MET cc_start: 0.7623 (mmt) cc_final: 0.6619 (tmm) REVERT: Y 150 ARG cc_start: 0.7321 (mtt180) cc_final: 0.6760 (tmm160) REVERT: Y 180 ASN cc_start: 0.8302 (m-40) cc_final: 0.7387 (m-40) REVERT: F 190 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7131 (mttt) REVERT: F 198 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8242 (tp) REVERT: E 149 MET cc_start: 0.7086 (mmt) cc_final: 0.6533 (mmt) REVERT: E 150 ARG cc_start: 0.7362 (mtt180) cc_final: 0.6687 (tmm160) REVERT: E 172 ASN cc_start: 0.7937 (m110) cc_final: 0.7683 (p0) REVERT: E 180 ASN cc_start: 0.8398 (m-40) cc_final: 0.7672 (m-40) REVERT: E 234 MET cc_start: 0.7825 (mtp) cc_final: 0.7545 (mtm) REVERT: C 57 TYR cc_start: 0.8472 (m-10) cc_final: 0.7998 (m-10) REVERT: C 66 GLN cc_start: 0.6323 (tt0) cc_final: 0.5962 (tp40) REVERT: C 190 LYS cc_start: 0.7762 (mtpt) cc_final: 0.6980 (mttt) REVERT: B 116 ILE cc_start: 0.8658 (tp) cc_final: 0.8332 (tp) REVERT: B 180 ASN cc_start: 0.8486 (m-40) cc_final: 0.7966 (m-40) outliers start: 55 outliers final: 48 residues processed: 257 average time/residue: 0.2150 time to fit residues: 83.2109 Evaluate side-chains 263 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 214 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 94 GLU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 198 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 247 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 68 optimal weight: 0.0070 chunk 101 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 121 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12000 Z= 0.209 Angle : 0.685 15.163 16320 Z= 0.354 Chirality : 0.043 0.159 1986 Planarity : 0.005 0.054 2028 Dihedral : 5.773 49.844 1724 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 4.08 % Allowed : 18.55 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.92 (0.21), residues: 1548 helix: -0.44 (0.16), residues: 1137 sheet: None (None), residues: 0 loop : -3.49 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 210 HIS 0.006 0.001 HIS B 140 PHE 0.025 0.001 PHE B 12 TYR 0.010 0.001 TYR Z 57 ARG 0.008 0.001 ARG C 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 1.252 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9120 (mm) cc_final: 0.8790 (mt) REVERT: Y 149 MET cc_start: 0.7600 (mmt) cc_final: 0.6599 (tmm) REVERT: Y 150 ARG cc_start: 0.7306 (mtt180) cc_final: 0.6718 (tmm160) REVERT: Y 180 ASN cc_start: 0.8262 (m-40) cc_final: 0.7036 (m-40) REVERT: Y 184 ILE cc_start: 0.8400 (mt) cc_final: 0.8020 (mp) REVERT: F 143 MET cc_start: 0.8649 (mmt) cc_final: 0.8293 (mmm) REVERT: F 190 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7121 (mttt) REVERT: F 198 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8251 (tp) REVERT: E 116 ILE cc_start: 0.8603 (tp) cc_final: 0.8293 (tp) REVERT: E 149 MET cc_start: 0.7076 (mmt) cc_final: 0.6534 (mmt) REVERT: E 172 ASN cc_start: 0.7926 (m110) cc_final: 0.7683 (p0) REVERT: E 180 ASN cc_start: 0.8340 (m-40) cc_final: 0.7633 (m-40) REVERT: E 234 MET cc_start: 0.7818 (mtp) cc_final: 0.7535 (mtm) REVERT: C 57 TYR cc_start: 0.8445 (m-10) cc_final: 0.8016 (m-10) REVERT: C 66 GLN cc_start: 0.6319 (tt0) cc_final: 0.5952 (tp40) REVERT: C 190 LYS cc_start: 0.7825 (mtpt) cc_final: 0.7020 (mttt) REVERT: C 209 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7944 (mttt) REVERT: B 116 ILE cc_start: 0.8655 (tp) cc_final: 0.8347 (tp) REVERT: B 180 ASN cc_start: 0.8378 (m-40) cc_final: 0.7671 (m-40) outliers start: 50 outliers final: 44 residues processed: 255 average time/residue: 0.2081 time to fit residues: 78.3928 Evaluate side-chains 261 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 216 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 94 GLU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 198 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 247 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119081 restraints weight = 16555.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122228 restraints weight = 9604.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124194 restraints weight = 6869.910| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12000 Z= 0.222 Angle : 0.704 15.047 16320 Z= 0.362 Chirality : 0.044 0.153 1986 Planarity : 0.005 0.055 2028 Dihedral : 5.716 49.706 1724 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 4.25 % Allowed : 18.46 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.79 (0.21), residues: 1548 helix: -0.36 (0.16), residues: 1140 sheet: None (None), residues: 0 loop : -3.40 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 210 HIS 0.005 0.001 HIS B 140 PHE 0.025 0.001 PHE E 12 TYR 0.036 0.001 TYR Z 57 ARG 0.007 0.001 ARG C 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2377.96 seconds wall clock time: 46 minutes 52.45 seconds (2812.45 seconds total)