Starting phenix.real_space_refine on Thu Feb 15 09:09:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/02_2024/6k1h_9906.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/02_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_9906/02_2024/6k1h_9906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/02_2024/6k1h_9906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/02_2024/6k1h_9906.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/02_2024/6k1h_9906.pdb" } 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 Residue "Z ARG 54": "NH1" <-> "NH2" Residue "Z ARG 96": "NH1" <-> "NH2" Residue "Z ARG 131": "NH1" <-> "NH2" Residue "Z ARG 221": "NH1" <-> "NH2" Residue "Y ARG 31": "NH1" <-> "NH2" Residue "Y ARG 247": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.28, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 2.4 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: 1.39 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: 2.97 Time building geometry restraints manager: 5.20 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: 97.95 - 105.30: 251 105.30 - 112.66: 6345 112.66 - 120.01: 4754 120.01 - 127.36: 4847 127.36 - 134.72: 123 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 2.440 nonbonded pdb=" OE1 GLU C 193 " pdb=" OH TYR B 245 " model vdw 2.032 2.440 ... (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 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: 0.340 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: 2.310 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.940 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.420 ------------------------------------------------------------------------------- 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 : 1.281 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: 0.2114 time to fit residues: 86.7574 Evaluate side-chains 222 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 214 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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: 0.9980 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 0.0170 chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12000 Z= 0.257 Angle : 0.760 10.312 16320 Z= 0.396 Chirality : 0.046 0.165 1986 Planarity : 0.006 0.059 2028 Dihedral : 9.265 59.070 1733 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.56 % Favored : 90.25 % Rotamer: Outliers : 3.02 % Allowed : 11.03 % Favored : 85.95 % 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: -3.76 (0.18), residues: 1548 helix: -1.85 (0.14), residues: 1119 sheet: None (None), residues: 0 loop : -3.91 (0.22), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 35 HIS 0.004 0.001 HIS B 140 PHE 0.021 0.002 PHE C 25 TYR 0.012 0.001 TYR E 194 ARG 0.017 0.001 ARG B 150 *********************** 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 273 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: Y 52 ILE cc_start: 0.8758 (mt) cc_final: 0.8519 (mt) REVERT: Y 149 MET cc_start: 0.7385 (mmt) cc_final: 0.6789 (tmm) REVERT: Y 150 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7092 (tmm160) REVERT: Y 180 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8131 (m-40) REVERT: Y 184 ILE cc_start: 0.8588 (mt) cc_final: 0.8298 (mp) REVERT: F 156 LEU cc_start: 0.9222 (mm) cc_final: 0.8963 (mt) REVERT: F 190 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7131 (mttt) REVERT: E 51 ILE cc_start: 0.8955 (mt) cc_final: 0.8656 (mp) REVERT: E 149 MET cc_start: 0.7151 (mmt) cc_final: 0.6476 (tmm) REVERT: E 150 ARG cc_start: 0.7638 (mtt180) cc_final: 0.6834 (tmm160) REVERT: E 170 MET cc_start: 0.6778 (tpt) cc_final: 0.6464 (tpt) REVERT: E 234 MET cc_start: 0.7942 (mtp) cc_final: 0.7587 (mtm) REVERT: C 143 MET cc_start: 0.8585 (mmt) cc_final: 0.8360 (mmt) REVERT: C 190 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7142 (mttt) REVERT: B 64 MET cc_start: 0.8355 (pmm) cc_final: 0.7526 (pmm) REVERT: B 180 ASN cc_start: 0.8641 (m-40) cc_final: 0.7972 (m-40) outliers start: 37 outliers final: 26 residues processed: 253 average time/residue: 0.2337 time to fit residues: 87.0270 Evaluate side-chains 227 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 232 THR Chi-restraints excluded: chain Z residue 233 THR 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 61 ASN Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 232 THR 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 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 C residue 233 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 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: 1.9990 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 123 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 71 HIS ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 HIS ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN E 223 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12000 Z= 0.246 Angle : 0.693 10.239 16320 Z= 0.364 Chirality : 0.044 0.175 1986 Planarity : 0.006 0.057 2028 Dihedral : 6.317 49.236 1716 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.98 % Favored : 90.83 % Rotamer: Outliers : 3.35 % Allowed : 14.71 % Favored : 81.94 % 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: -3.19 (0.19), residues: 1548 helix: -1.41 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -3.82 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 210 HIS 0.003 0.001 HIS B 30 PHE 0.022 0.002 PHE E 12 TYR 0.015 0.001 TYR E 194 ARG 0.003 0.001 ARG C 70 *********************** 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 265 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 224 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: Z 156 LEU cc_start: 0.9176 (mm) cc_final: 0.8886 (mt) REVERT: Y 149 MET cc_start: 0.7583 (mmt) cc_final: 0.7055 (tmm) REVERT: Y 150 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7245 (tmm160) REVERT: Y 184 ILE cc_start: 0.8577 (mt) cc_final: 0.8262 (mp) REVERT: Y 201 MET cc_start: 0.7898 (ptp) cc_final: 0.7575 (ptp) REVERT: F 156 LEU cc_start: 0.9202 (mm) cc_final: 0.8872 (mt) REVERT: F 190 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7132 (mttt) REVERT: F 209 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8199 (ttmt) REVERT: E 64 MET cc_start: 0.8697 (pmm) cc_final: 0.8222 (pmm) REVERT: E 149 MET cc_start: 0.7224 (mmt) cc_final: 0.6719 (tmm) REVERT: E 150 ARG cc_start: 0.7610 (mtt180) cc_final: 0.6785 (tmm160) REVERT: E 234 MET cc_start: 0.7890 (mtp) cc_final: 0.7562 (mtm) REVERT: C 143 MET cc_start: 0.8629 (mmt) cc_final: 0.8353 (mmt) REVERT: C 190 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7130 (mttt) REVERT: B 64 MET cc_start: 0.8518 (pmm) cc_final: 0.7874 (pmm) REVERT: B 180 ASN cc_start: 0.8555 (m-40) cc_final: 0.7910 (m-40) outliers start: 41 outliers final: 32 residues processed: 243 average time/residue: 0.2406 time to fit residues: 85.1562 Evaluate side-chains 231 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 129 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS 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 121 VAL Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 232 THR 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 201 MET Chi-restraints excluded: chain E residue 220 THR 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 137 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 THR 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 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 0.2980 chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** 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** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12000 Z= 0.267 Angle : 0.692 10.766 16320 Z= 0.358 Chirality : 0.044 0.174 1986 Planarity : 0.005 0.058 2028 Dihedral : 6.137 39.350 1715 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.17 % Favored : 90.63 % Rotamer: Outliers : 4.41 % Allowed : 16.09 % Favored : 79.49 % 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: -2.88 (0.20), residues: 1548 helix: -1.20 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -3.64 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 210 HIS 0.003 0.001 HIS C 71 PHE 0.023 0.002 PHE E 12 TYR 0.010 0.001 TYR E 194 ARG 0.008 0.001 ARG F 69 *********************** 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 275 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 221 time to evaluate : 1.219 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9138 (mm) cc_final: 0.8825 (mt) REVERT: Z 209 LYS cc_start: 0.8296 (ttmt) cc_final: 0.8047 (ttmt) REVERT: Y 28 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8532 (mm110) REVERT: Y 149 MET cc_start: 0.7584 (mmt) cc_final: 0.7128 (tmm) REVERT: Y 150 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7245 (tmm160) REVERT: F 156 LEU cc_start: 0.9206 (mm) cc_final: 0.8904 (mt) REVERT: F 190 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7081 (mttt) REVERT: E 51 ILE cc_start: 0.8838 (mt) cc_final: 0.8575 (mp) REVERT: E 64 MET cc_start: 0.8635 (pmm) cc_final: 0.8327 (pmm) REVERT: E 149 MET cc_start: 0.7138 (mmt) cc_final: 0.6719 (tmm) REVERT: E 150 ARG cc_start: 0.7642 (mtt180) cc_final: 0.6793 (tmm160) REVERT: E 172 ASN cc_start: 0.7892 (m110) cc_final: 0.7646 (p0) REVERT: E 234 MET cc_start: 0.7848 (mtp) cc_final: 0.7521 (mtm) REVERT: C 143 MET cc_start: 0.8640 (mmt) cc_final: 0.8367 (mmt) REVERT: C 190 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7120 (mttt) REVERT: B 64 MET cc_start: 0.8528 (pmm) cc_final: 0.7957 (pmm) REVERT: B 168 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7065 (mm-40) REVERT: B 180 ASN cc_start: 0.8521 (m-40) cc_final: 0.7877 (m-40) REVERT: B 220 THR cc_start: 0.8884 (m) cc_final: 0.8629 (p) outliers start: 54 outliers final: 44 residues processed: 250 average time/residue: 0.2108 time to fit residues: 77.4322 Evaluate side-chains 250 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 129 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 233 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 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 129 THR 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 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 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 E residue 221 ASN Chi-restraints excluded: chain C residue 30 LEU 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 137 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 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 160 LEU 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: 4.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 12000 Z= 0.455 Angle : 0.780 10.034 16320 Z= 0.406 Chirality : 0.048 0.174 1986 Planarity : 0.006 0.063 2028 Dihedral : 6.378 40.287 1715 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.37 % Favored : 88.44 % Rotamer: Outliers : 7.35 % Allowed : 15.20 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -3.14 (0.20), residues: 1548 helix: -1.38 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -3.81 (0.24), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 210 HIS 0.004 0.001 HIS F 71 PHE 0.024 0.002 PHE B 12 TYR 0.011 0.001 TYR B 194 ARG 0.006 0.001 ARG B 202 *********************** 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 300 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 210 time to evaluate : 1.221 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9229 (mm) cc_final: 0.8949 (mt) REVERT: Y 149 MET cc_start: 0.7547 (mmt) cc_final: 0.7110 (tmm) REVERT: Y 150 ARG cc_start: 0.7709 (mtt180) cc_final: 0.7318 (tmm160) REVERT: F 156 LEU cc_start: 0.9260 (mm) cc_final: 0.8932 (mt) REVERT: F 190 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7141 (mttt) REVERT: E 150 ARG cc_start: 0.7509 (mtt180) cc_final: 0.7030 (tmm160) REVERT: E 234 MET cc_start: 0.7999 (mtp) cc_final: 0.7682 (mtm) REVERT: C 190 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7246 (mttt) REVERT: B 20 MET cc_start: 0.7629 (mmm) cc_final: 0.7402 (mmt) REVERT: B 168 GLN cc_start: 0.7460 (mm-40) cc_final: 0.7050 (mm-40) REVERT: B 180 ASN cc_start: 0.8697 (m-40) cc_final: 0.8071 (m-40) REVERT: B 220 THR cc_start: 0.9089 (m) cc_final: 0.8800 (p) outliers start: 90 outliers final: 69 residues processed: 266 average time/residue: 0.2194 time to fit residues: 85.3380 Evaluate side-chains 273 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 204 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 21 ILE 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 129 THR 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 Z residue 233 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 115 THR Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 162 VAL 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 61 ASN 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 159 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 183 MET 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 48 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 142 SER 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 201 MET Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain C residue 30 LEU 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 129 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 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 115 THR Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU 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: 0.8980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.0570 chunk 148 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 142 optimal weight: 0.0020 overall best weight: 0.4506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 90 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 121 GLN E 172 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2567 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= 0.202 Angle : 0.657 10.364 16320 Z= 0.345 Chirality : 0.043 0.172 1986 Planarity : 0.005 0.060 2028 Dihedral : 5.953 39.322 1715 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.33 % Favored : 91.47 % Rotamer: Outliers : 4.98 % Allowed : 18.06 % Favored : 76.96 % 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: -2.60 (0.20), residues: 1548 helix: -0.93 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -3.77 (0.23), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 127 HIS 0.005 0.001 HIS B 140 PHE 0.023 0.001 PHE B 12 TYR 0.008 0.001 TYR Y 194 ARG 0.003 0.000 ARG B 150 *********************** 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 289 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 228 time to evaluate : 1.354 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9139 (mm) cc_final: 0.8854 (mt) REVERT: Y 20 MET cc_start: 0.7669 (mmm) cc_final: 0.7199 (mmm) REVERT: Y 149 MET cc_start: 0.7587 (mmt) cc_final: 0.6925 (tmm) REVERT: Y 150 ARG cc_start: 0.7630 (mtt180) cc_final: 0.7094 (tmm160) REVERT: Y 172 ASN cc_start: 0.7885 (m110) cc_final: 0.7497 (p0) REVERT: F 183 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7235 (mtp) REVERT: F 190 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7047 (mttt) REVERT: E 51 ILE cc_start: 0.8814 (mt) cc_final: 0.8569 (mp) REVERT: E 150 ARG cc_start: 0.7635 (mtt180) cc_final: 0.6794 (tmm160) REVERT: E 234 MET cc_start: 0.7920 (mtp) cc_final: 0.7656 (mtm) REVERT: C 190 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7220 (mttt) REVERT: B 20 MET cc_start: 0.7589 (mmm) cc_final: 0.7023 (mmt) REVERT: B 24 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8002 (mp) REVERT: B 116 ILE cc_start: 0.8755 (tp) cc_final: 0.8490 (tp) REVERT: B 180 ASN cc_start: 0.8481 (m-40) cc_final: 0.7828 (m-40) REVERT: B 220 THR cc_start: 0.8885 (m) cc_final: 0.8614 (p) outliers start: 61 outliers final: 42 residues processed: 263 average time/residue: 0.2124 time to fit residues: 81.7225 Evaluate side-chains 253 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 26 LEU 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 129 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 233 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 90 GLN Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 191 VAL 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 183 MET Chi-restraints excluded: chain F residue 232 THR 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 160 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain C residue 30 LEU 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 129 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 189 ILE 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: 4.9990 chunk 84 optimal weight: 0.7980 chunk 108 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 147 optimal weight: 0.0570 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 90 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 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** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2767 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= 0.207 Angle : 0.648 10.421 16320 Z= 0.340 Chirality : 0.043 0.159 1986 Planarity : 0.005 0.056 2028 Dihedral : 5.690 39.176 1715 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.50 % Favored : 90.44 % Rotamer: Outliers : 5.31 % Allowed : 18.46 % Favored : 76.23 % 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: -2.38 (0.21), residues: 1548 helix: -0.79 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -3.60 (0.24), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 127 HIS 0.005 0.001 HIS B 140 PHE 0.025 0.001 PHE Y 12 TYR 0.007 0.001 TYR Y 194 ARG 0.002 0.000 ARG F 221 *********************** 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 293 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 228 time to evaluate : 1.162 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9150 (mm) cc_final: 0.8852 (mt) REVERT: Y 149 MET cc_start: 0.7652 (mmt) cc_final: 0.6849 (tmm) REVERT: Y 150 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7058 (tmm160) REVERT: Y 172 ASN cc_start: 0.7890 (m110) cc_final: 0.7501 (p0) REVERT: F 183 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7164 (mtp) REVERT: F 190 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7128 (mttt) REVERT: F 198 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8193 (tp) REVERT: E 51 ILE cc_start: 0.8815 (mt) cc_final: 0.8545 (mp) REVERT: E 150 ARG cc_start: 0.7528 (mtt180) cc_final: 0.6639 (tmm160) REVERT: E 234 MET cc_start: 0.7867 (mtp) cc_final: 0.7562 (mtm) REVERT: B 98 LEU cc_start: 0.9327 (tt) cc_final: 0.9106 (tt) REVERT: B 116 ILE cc_start: 0.8736 (tp) cc_final: 0.8496 (tp) REVERT: B 180 ASN cc_start: 0.8531 (m-40) cc_final: 0.7907 (m-40) REVERT: B 220 THR cc_start: 0.8836 (m) cc_final: 0.8598 (p) outliers start: 65 outliers final: 47 residues processed: 267 average time/residue: 0.2189 time to fit residues: 85.2244 Evaluate side-chains 261 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 212 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 26 LEU 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 129 THR Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 233 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 90 GLN Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 50 VAL 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 129 THR Chi-restraints excluded: chain F residue 147 LEU 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 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 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 26 LEU 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 129 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 241 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 44 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 240 GLN Y 90 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 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** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12000 Z= 0.218 Angle : 0.660 10.539 16320 Z= 0.342 Chirality : 0.043 0.177 1986 Planarity : 0.005 0.053 2028 Dihedral : 5.571 39.919 1714 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 5.23 % Allowed : 18.79 % Favored : 75.98 % 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: -2.27 (0.21), residues: 1548 helix: -0.72 (0.16), residues: 1140 sheet: None (None), residues: 0 loop : -3.56 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Z 210 HIS 0.006 0.001 HIS E 140 PHE 0.025 0.001 PHE E 12 TYR 0.010 0.001 TYR Z 57 ARG 0.009 0.001 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 292 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 228 time to evaluate : 1.340 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9156 (mm) cc_final: 0.8860 (mt) REVERT: Z 209 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7903 (ttmt) REVERT: Y 149 MET cc_start: 0.7627 (mmt) cc_final: 0.6833 (tmm) REVERT: Y 150 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7038 (tmm160) REVERT: Y 180 ASN cc_start: 0.8189 (m-40) cc_final: 0.7830 (m-40) REVERT: F 183 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7069 (mtp) REVERT: F 190 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7116 (mttt) REVERT: F 198 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8224 (tp) REVERT: E 28 GLN cc_start: 0.8825 (mm110) cc_final: 0.8572 (mm-40) REVERT: E 51 ILE cc_start: 0.8691 (mt) cc_final: 0.8415 (mp) REVERT: E 116 ILE cc_start: 0.8638 (tp) cc_final: 0.8334 (tp) REVERT: E 150 ARG cc_start: 0.7507 (mtt180) cc_final: 0.6594 (tmm160) REVERT: E 234 MET cc_start: 0.7887 (mtp) cc_final: 0.7558 (mtm) REVERT: B 98 LEU cc_start: 0.9292 (tt) cc_final: 0.9083 (tt) REVERT: B 116 ILE cc_start: 0.8774 (tp) cc_final: 0.8543 (tp) REVERT: B 172 ASN cc_start: 0.7540 (m110) cc_final: 0.7319 (p0) REVERT: B 180 ASN cc_start: 0.8556 (m-40) cc_final: 0.7972 (m-40) REVERT: B 220 THR cc_start: 0.8812 (m) cc_final: 0.8593 (p) outliers start: 64 outliers final: 51 residues processed: 263 average time/residue: 0.2184 time to fit residues: 84.8031 Evaluate side-chains 269 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 216 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 26 LEU 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 129 THR Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 240 GLN 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 90 GLN Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 50 VAL 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 129 THR Chi-restraints excluded: chain F residue 147 LEU 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 177 VAL Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain C residue 26 LEU 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 129 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 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 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 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 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 90 GLN ** F 41 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** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12000 Z= 0.238 Angle : 0.663 10.540 16320 Z= 0.344 Chirality : 0.043 0.168 1986 Planarity : 0.005 0.052 2028 Dihedral : 5.535 39.653 1714 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.74 % Allowed : 19.20 % Favored : 76.06 % 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: -2.22 (0.21), residues: 1548 helix: -0.69 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -3.51 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 210 HIS 0.005 0.001 HIS B 140 PHE 0.024 0.001 PHE B 12 TYR 0.018 0.001 TYR Z 57 ARG 0.007 0.000 ARG F 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 280 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 222 time to evaluate : 1.298 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9152 (mm) cc_final: 0.8845 (mt) REVERT: Y 149 MET cc_start: 0.7626 (mmt) cc_final: 0.6837 (tmm) REVERT: Y 150 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7175 (tmm160) REVERT: Y 180 ASN cc_start: 0.8187 (m-40) cc_final: 0.7458 (m-40) REVERT: Y 184 ILE cc_start: 0.8473 (mt) cc_final: 0.8092 (mp) REVERT: F 183 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7212 (mtp) REVERT: F 190 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7117 (mttt) REVERT: F 198 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8304 (tp) REVERT: E 51 ILE cc_start: 0.8778 (mt) cc_final: 0.8513 (mp) REVERT: E 150 ARG cc_start: 0.7517 (mtt180) cc_final: 0.6586 (tmm160) REVERT: E 234 MET cc_start: 0.7934 (mtp) cc_final: 0.7621 (mtm) REVERT: B 116 ILE cc_start: 0.8775 (tp) cc_final: 0.8546 (tp) REVERT: B 172 ASN cc_start: 0.7538 (m110) cc_final: 0.7335 (p0) REVERT: B 180 ASN cc_start: 0.8516 (m-40) cc_final: 0.8004 (m-40) REVERT: B 220 THR cc_start: 0.8814 (m) cc_final: 0.8599 (p) outliers start: 58 outliers final: 50 residues processed: 256 average time/residue: 0.2089 time to fit residues: 78.8750 Evaluate side-chains 267 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 215 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 26 LEU 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 129 THR Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 233 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 191 VAL Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 50 VAL 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 129 THR Chi-restraints excluded: chain F residue 147 LEU 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 23 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 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 221 ASN Chi-restraints excluded: chain C residue 26 LEU 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 129 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 152 optimal weight: 0.0000 chunk 140 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 240 GLN Y 90 GLN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN B 121 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12000 Z= 0.197 Angle : 0.670 14.383 16320 Z= 0.342 Chirality : 0.042 0.154 1986 Planarity : 0.005 0.052 2028 Dihedral : 5.404 38.912 1714 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.49 % Allowed : 19.53 % Favored : 75.98 % 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: -1.97 (0.21), residues: 1548 helix: -0.47 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -3.49 (0.24), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 127 HIS 0.006 0.001 HIS B 140 PHE 0.025 0.001 PHE E 12 TYR 0.018 0.001 TYR Z 57 ARG 0.007 0.001 ARG F 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: 55 poor density : 220 time to evaluate : 1.329 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9066 (mm) cc_final: 0.8736 (mt) REVERT: Y 149 MET cc_start: 0.7495 (mmt) cc_final: 0.6615 (tmm) REVERT: Y 150 ARG cc_start: 0.7346 (mtt180) cc_final: 0.6766 (tmm160) REVERT: Y 180 ASN cc_start: 0.8236 (m-40) cc_final: 0.7012 (m110) REVERT: Y 184 ILE cc_start: 0.8432 (mt) cc_final: 0.8042 (mp) REVERT: F 156 LEU cc_start: 0.8837 (mm) cc_final: 0.8455 (mt) REVERT: F 183 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7166 (mtp) REVERT: F 190 LYS cc_start: 0.7870 (mtpt) cc_final: 0.6991 (mttt) REVERT: F 198 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8259 (tp) REVERT: E 51 ILE cc_start: 0.8652 (mt) cc_final: 0.8371 (mp) REVERT: E 116 ILE cc_start: 0.8590 (tp) cc_final: 0.8299 (tp) REVERT: E 150 ARG cc_start: 0.7317 (mtt180) cc_final: 0.6454 (tmm160) REVERT: E 180 ASN cc_start: 0.8371 (m-40) cc_final: 0.7655 (m-40) REVERT: E 234 MET cc_start: 0.7835 (mtp) cc_final: 0.7530 (mtm) REVERT: B 116 ILE cc_start: 0.8700 (tp) cc_final: 0.8385 (tp) REVERT: B 172 ASN cc_start: 0.7537 (m110) cc_final: 0.7331 (p0) REVERT: B 180 ASN cc_start: 0.8410 (m-40) cc_final: 0.7956 (m-40) outliers start: 55 outliers final: 47 residues processed: 254 average time/residue: 0.2002 time to fit residues: 75.8566 Evaluate side-chains 260 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 211 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 26 LEU 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 129 THR Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 240 GLN 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 90 GLN Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 147 LEU 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 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 160 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 30 LEU 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 129 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 214 ASN ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119066 restraints weight = 16531.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122246 restraints weight = 9770.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.123992 restraints weight = 7008.578| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12000 Z= 0.210 Angle : 0.671 14.563 16320 Z= 0.343 Chirality : 0.043 0.151 1986 Planarity : 0.005 0.052 2028 Dihedral : 5.359 39.308 1714 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.92 % Allowed : 20.26 % Favored : 75.82 % 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: -1.81 (0.21), residues: 1548 helix: -0.38 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -3.34 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 127 HIS 0.005 0.001 HIS B 140 PHE 0.024 0.001 PHE B 12 TYR 0.017 0.001 TYR Z 57 ARG 0.007 0.001 ARG F 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.20 seconds wall clock time: 44 minutes 50.73 seconds (2690.73 seconds total)