Starting phenix.real_space_refine (version: dev) on Tue Apr 5 06:45:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/04_2022/6k1h_9906_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/04_2022/6k1h_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_9906/04_2022/6k1h_9906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/04_2022/6k1h_9906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/04_2022/6k1h_9906_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1h_9906/04_2022/6k1h_9906_neut.pdb" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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 "Y ARG 31": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 11556 Number of models: 1 Model: "" Number of chains: 9 Chain: "Z" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2051 Classifications: {'peptide': 266} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 252} Chain: "Y" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1789 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 236, 'PCIS': 1} Chain: "C" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2051 Classifications: {'peptide': 266} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 252} Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1789 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 236, 'PCIS': 1} Chain: "F" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2051 Classifications: {'peptide': 266} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 252} Chain: "E" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1789 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 236, 'PCIS': 1} 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: "C" 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} Time building chain proxies: 6.93, per 1000 atoms: 0.60 Number of scatterers: 11556 At special positions: 0 Unit cell: (128.448, 124.434, 92.322, 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 2001 8.00 N 1923 7.00 C 7557 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: 4.98 Conformation dependent library (CDL) restraints added in 1.8 seconds 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2742 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 0 sheets defined 67.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'Z' and resid 21 through 26 Processing helix chain 'Z' and resid 41 through 49 Processing helix chain 'Z' and resid 49 through 56 removed outlier: 4.061A pdb=" N ARG Z 55 " --> pdb=" O PRO Z 51 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU Z 56 " --> pdb=" O ALA Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 65 through 71 removed outlier: 3.560A pdb=" N ARG Z 69 " --> pdb=" O LYS Z 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 95 removed outlier: 3.673A pdb=" N ALA Z 91 " --> pdb=" O GLY Z 87 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU Z 93 " --> pdb=" O THR Z 89 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU Z 94 " --> pdb=" O LEU Z 90 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN Z 95 " --> pdb=" O ALA Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 123 removed outlier: 4.195A pdb=" N ASN Z 108 " --> pdb=" O ASP Z 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS Z 111 " --> pdb=" O ILE Z 107 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY Z 116 " --> pdb=" O VAL Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix removed outlier: 3.793A pdb=" N GLY Z 120 " --> pdb=" O GLY Z 116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP Z 123 " --> pdb=" O ALA Z 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 138 removed outlier: 3.688A pdb=" N ALA Z 136 " --> pdb=" O PRO Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 140 through 145 removed outlier: 4.434A pdb=" N SER Z 144 " --> pdb=" O GLY Z 140 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 157 removed outlier: 3.721A pdb=" N PHE Z 153 " --> pdb=" O GLY Z 149 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE Z 154 " --> pdb=" O PRO Z 150 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE Z 155 " --> pdb=" O LEU Z 151 " (cutoff:3.500A) Processing helix chain 'Z' and resid 159 through 174 removed outlier: 3.542A pdb=" N THR Z 164 " --> pdb=" O VAL Z 160 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG Z 165 " --> pdb=" O ARG Z 161 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR Z 167 " --> pdb=" O ALA Z 163 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY Z 168 " --> pdb=" O THR Z 164 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR Z 171 " --> pdb=" O TYR Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 176 through 180 removed outlier: 3.678A pdb=" N ILE Z 179 " --> pdb=" O GLY Z 176 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 192 removed outlier: 3.575A pdb=" N LYS Z 190 " --> pdb=" O GLY Z 186 " (cutoff:3.500A) Processing helix chain 'Z' and resid 194 through 209 removed outlier: 4.113A pdb=" N LEU Z 200 " --> pdb=" O SER Z 196 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET Z 203 " --> pdb=" O GLY Z 199 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA Z 205 " --> pdb=" O PHE Z 201 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL Z 207 " --> pdb=" O MET Z 203 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN Z 208 " --> pdb=" O GLY Z 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 239 Processing helix chain 'Z' and resid 244 through 258 removed outlier: 3.587A pdb=" N PHE Z 252 " --> pdb=" O LEU Z 248 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET Z 255 " --> pdb=" O THR Z 251 " (cutoff:3.500A) Processing helix chain 'Z' and resid 263 through 266 Processing helix chain 'Z' and resid 267 through 281 removed outlier: 3.926A pdb=" N ILE Z 276 " --> pdb=" O PHE Z 272 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR Z 279 " --> pdb=" O GLY Z 275 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA Z 280 " --> pdb=" O ILE Z 276 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS Z 281 " --> pdb=" O ALA Z 277 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 21 removed outlier: 4.224A pdb=" N VAL Y 9 " --> pdb=" O THR Y 5 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY Y 19 " --> pdb=" O ALA Y 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 44 removed outlier: 4.555A pdb=" N VAL Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL Y 42 " --> pdb=" O LEU Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 60 removed outlier: 3.507A pdb=" N ILE Y 51 " --> pdb=" O LYS Y 47 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE Y 52 " --> pdb=" O THR Y 48 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU Y 57 " --> pdb=" O GLY Y 53 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 84 Processing helix chain 'Y' and resid 91 through 117 removed outlier: 3.768A pdb=" N GLY Y 95 " --> pdb=" O SER Y 91 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE Y 96 " --> pdb=" O ILE Y 92 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA Y 97 " --> pdb=" O GLY Y 93 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE Y 100 " --> pdb=" O ILE Y 96 " (cutoff:3.500A) Proline residue: Y 101 - end of helix removed outlier: 3.795A pdb=" N GLN Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL Y 108 " --> pdb=" O ALA Y 104 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE Y 112 " --> pdb=" O VAL Y 108 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG Y 114 " --> pdb=" O THR Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 123 removed outlier: 3.522A pdb=" N HIS Y 122 " --> pdb=" O VAL Y 118 " (cutoff:3.500A) Processing helix chain 'Y' and resid 124 through 129 Processing helix chain 'Y' and resid 133 through 143 removed outlier: 4.252A pdb=" N ILE Y 139 " --> pdb=" O ALA Y 135 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL Y 141 " --> pdb=" O SER Y 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER Y 142 " --> pdb=" O TRP Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 151 removed outlier: 4.007A pdb=" N VAL Y 151 " --> pdb=" O ALA Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 175 through 181 Processing helix chain 'Y' and resid 184 through 188 Processing helix chain 'Y' and resid 189 through 201 removed outlier: 3.894A pdb=" N GLY Y 193 " --> pdb=" O ILE Y 189 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL Y 197 " --> pdb=" O GLY Y 193 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET Y 200 " --> pdb=" O MET Y 196 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 220 removed outlier: 3.820A pdb=" N TYR Y 211 " --> pdb=" O MET Y 207 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA Y 217 " --> pdb=" O GLY Y 213 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA Y 218 " --> pdb=" O PHE Y 214 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE Y 219 " --> pdb=" O VAL Y 215 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR Y 220 " --> pdb=" O THR Y 216 " (cutoff:3.500A) Processing helix chain 'Y' and resid 225 through 241 removed outlier: 3.549A pdb=" N GLY Y 231 " --> pdb=" O LEU Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 242 through 246 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 49 through 56 removed outlier: 4.061A pdb=" N ARG C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 removed outlier: 3.560A pdb=" N ARG C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.673A pdb=" N ALA C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 123 removed outlier: 4.194A pdb=" N ASN C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Proline residue: C 117 - end of helix removed outlier: 3.792A pdb=" N GLY C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 138 removed outlier: 3.688A pdb=" N ALA C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 removed outlier: 4.435A pdb=" N SER C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 157 removed outlier: 3.720A pdb=" N PHE C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 174 removed outlier: 3.542A pdb=" N THR C 164 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR C 171 " --> pdb=" O TYR C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.679A pdb=" N ILE C 179 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.575A pdb=" N LYS C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 209 removed outlier: 4.112A pdb=" N LEU C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET C 203 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 207 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.587A pdb=" N PHE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 266 Processing helix chain 'C' and resid 267 through 281 removed outlier: 3.926A pdb=" N ILE C 276 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR C 279 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C 280 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 21 removed outlier: 4.223A pdb=" N VAL B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 removed outlier: 4.555A pdb=" N VAL B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 60 removed outlier: 3.507A pdb=" N ILE B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 91 through 117 removed outlier: 3.769A pdb=" N GLY B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 96 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Proline residue: B 101 - end of helix removed outlier: 3.795A pdb=" N GLN B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.521A pdb=" N HIS B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 133 through 143 removed outlier: 4.251A pdb=" N ILE B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 142 " --> pdb=" O TRP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.007A pdb=" N VAL B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 189 through 201 removed outlier: 3.895A pdb=" N GLY B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.820A pdb=" N TYR B 211 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 241 removed outlier: 3.550A pdb=" N GLY B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 41 through 49 Processing helix chain 'F' and resid 49 through 56 removed outlier: 4.061A pdb=" N ARG F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 71 removed outlier: 3.560A pdb=" N ARG F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.673A pdb=" N ALA F 91 " --> pdb=" O GLY F 87 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 123 removed outlier: 4.194A pdb=" N ASN F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS F 111 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Proline residue: F 117 - end of helix removed outlier: 3.791A pdb=" N GLY F 120 " --> pdb=" O GLY F 116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 138 removed outlier: 3.688A pdb=" N ALA F 136 " --> pdb=" O PRO F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 145 removed outlier: 4.434A pdb=" N SER F 144 " --> pdb=" O GLY F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 157 removed outlier: 3.720A pdb=" N PHE F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE F 154 " --> pdb=" O PRO F 150 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 174 removed outlier: 3.542A pdb=" N THR F 164 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY F 168 " --> pdb=" O THR F 164 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR F 171 " --> pdb=" O TYR F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 180 removed outlier: 3.679A pdb=" N ILE F 179 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 192 removed outlier: 3.575A pdb=" N LYS F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 209 removed outlier: 4.111A pdb=" N LEU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET F 203 " --> pdb=" O GLY F 199 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA F 205 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 207 " --> pdb=" O MET F 203 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.587A pdb=" N PHE F 252 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET F 255 " --> pdb=" O THR F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 266 Processing helix chain 'F' and resid 267 through 281 removed outlier: 3.926A pdb=" N ILE F 276 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR F 279 " --> pdb=" O GLY F 275 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA F 280 " --> pdb=" O ILE F 276 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N CYS F 281 " --> pdb=" O ALA F 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 21 removed outlier: 4.223A pdb=" N VAL E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU E 10 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 44 removed outlier: 4.555A pdb=" N VAL E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 60 removed outlier: 3.506A pdb=" N ILE E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 57 " --> pdb=" O GLY E 53 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 84 Processing helix chain 'E' and resid 91 through 117 removed outlier: 3.769A pdb=" N GLY E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE E 96 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 100 " --> pdb=" O ILE E 96 " (cutoff:3.500A) Proline residue: E 101 - end of helix removed outlier: 3.795A pdb=" N GLN E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 123 removed outlier: 3.522A pdb=" N HIS E 122 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 133 through 143 removed outlier: 4.251A pdb=" N ILE E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER E 142 " --> pdb=" O TRP E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 4.007A pdb=" N VAL E 151 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 175 through 181 Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.894A pdb=" N GLY E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET E 200 " --> pdb=" O MET E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 220 removed outlier: 3.819A pdb=" N TYR E 211 " --> pdb=" O MET E 207 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA E 217 " --> pdb=" O GLY E 213 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 218 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE E 219 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E 220 " --> pdb=" O THR E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 241 removed outlier: 3.548A pdb=" N GLY E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 246 441 hydrogen bonds defined for protein. 1260 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: 2.92 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3541 1.34 - 1.45: 1826 1.45 - 1.57: 6285 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 11787 Sorted by residual: bond pdb=" C ILE B 153 " pdb=" N PRO B 154 " ideal model delta sigma weight residual 1.334 1.376 -0.042 8.40e-03 1.42e+04 2.50e+01 bond pdb=" C ILE E 153 " pdb=" N PRO E 154 " ideal model delta sigma weight residual 1.334 1.375 -0.042 8.40e-03 1.42e+04 2.47e+01 bond pdb=" C ILE Y 153 " pdb=" N PRO Y 154 " ideal model delta sigma weight residual 1.334 1.375 -0.042 8.40e-03 1.42e+04 2.47e+01 bond pdb=" C ARG Z 131 " pdb=" N PRO Z 132 " ideal model delta sigma weight residual 1.334 1.369 -0.036 8.40e-03 1.42e+04 1.79e+01 bond pdb=" C ARG F 131 " pdb=" N PRO F 132 " ideal model delta sigma weight residual 1.334 1.369 -0.035 8.40e-03 1.42e+04 1.79e+01 ... (remaining 11782 not shown) Histogram of bond angle deviations from ideal: 98.32 - 106.44: 377 106.44 - 114.56: 7020 114.56 - 122.68: 7757 122.68 - 130.81: 812 130.81 - 138.93: 72 Bond angle restraints: 16038 Sorted by residual: angle pdb=" N ILE F 267 " pdb=" CA ILE F 267 " pdb=" C ILE F 267 " ideal model delta sigma weight residual 112.96 106.22 6.74 1.00e+00 1.00e+00 4.54e+01 angle pdb=" N ILE C 267 " pdb=" CA ILE C 267 " pdb=" C ILE C 267 " ideal model delta sigma weight residual 112.96 106.22 6.74 1.00e+00 1.00e+00 4.54e+01 angle pdb=" N ILE Z 267 " pdb=" CA ILE Z 267 " pdb=" C ILE Z 267 " ideal model delta sigma weight residual 112.96 106.23 6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" C ILE Y 174 " pdb=" N PRO Y 175 " pdb=" CA PRO Y 175 " ideal model delta sigma weight residual 127.00 138.93 -11.93 2.40e+00 1.74e-01 2.47e+01 angle pdb=" C ILE E 174 " pdb=" N PRO E 175 " pdb=" CA PRO E 175 " ideal model delta sigma weight residual 127.00 138.91 -11.91 2.40e+00 1.74e-01 2.46e+01 ... (remaining 16033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 6480 14.82 - 29.63: 336 29.63 - 44.45: 57 44.45 - 59.26: 6 59.26 - 74.08: 3 Dihedral angle restraints: 6882 sinusoidal: 2580 harmonic: 4302 Sorted by residual: dihedral pdb=" CA ALA E 105 " pdb=" C ALA E 105 " pdb=" N GLY E 106 " pdb=" CA GLY E 106 " ideal model delta harmonic sigma weight residual 180.00 139.30 40.70 0 5.00e+00 4.00e-02 6.63e+01 dihedral pdb=" CA ALA B 105 " pdb=" C ALA B 105 " pdb=" N GLY B 106 " pdb=" CA GLY B 106 " ideal model delta harmonic sigma weight residual 180.00 139.31 40.69 0 5.00e+00 4.00e-02 6.62e+01 dihedral pdb=" CA ALA Y 105 " pdb=" C ALA Y 105 " pdb=" N GLY Y 106 " pdb=" CA GLY Y 106 " ideal model delta harmonic sigma weight residual 180.00 139.35 40.65 0 5.00e+00 4.00e-02 6.61e+01 ... (remaining 6879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1476 0.064 - 0.129: 408 0.129 - 0.193: 51 0.193 - 0.258: 6 0.258 - 0.322: 6 Chirality restraints: 1947 Sorted by residual: chirality pdb=" CB THR F 233 " pdb=" CA THR F 233 " pdb=" OG1 THR F 233 " pdb=" CG2 THR F 233 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB THR C 233 " pdb=" CA THR C 233 " pdb=" OG1 THR C 233 " pdb=" CG2 THR C 233 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB THR Z 233 " pdb=" CA THR Z 233 " pdb=" OG1 THR Z 233 " pdb=" CG2 THR Z 233 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 1944 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET Y 207 " 0.049 5.00e-02 4.00e+02 7.37e-02 8.69e+00 pdb=" N PRO Y 208 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO Y 208 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO Y 208 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 207 " -0.049 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO E 208 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO E 208 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 208 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 207 " 0.049 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO B 208 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.041 5.00e-02 4.00e+02 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 108 2.62 - 3.19: 9887 3.19 - 3.76: 17338 3.76 - 4.33: 25403 4.33 - 4.90: 39171 Nonbonded interactions: 91907 Sorted by model distance: nonbonded pdb=" NH1 ARG E 31 " pdb=" OE2 GLU E 57 " model vdw 2.051 2.520 nonbonded pdb=" NH1 ARG B 31 " pdb=" OE2 GLU B 57 " model vdw 2.051 2.520 nonbonded pdb=" NH1 ARG Y 31 " pdb=" OE2 GLU Y 57 " model vdw 2.051 2.520 nonbonded pdb=" OD2 ASP F 123 " pdb=" O6 MAN F 301 " model vdw 2.128 2.440 nonbonded pdb=" NH2 ARG F 70 " pdb=" OE2 GLU F 93 " model vdw 2.302 2.520 ... (remaining 91902 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 7557 2.51 5 N 1923 2.21 5 O 2001 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.790 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.110 Process input model: 32.450 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 0.101 11787 Z= 0.451 Angle : 1.136 11.927 16038 Z= 0.596 Chirality : 0.059 0.322 1947 Planarity : 0.008 0.074 1998 Dihedral : 9.935 74.080 4140 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -6.37 (0.14), residues: 1521 helix: -4.38 (0.08), residues: 957 sheet: None (None), residues: 0 loop : -3.61 (0.22), residues: 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 460 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 468 average time/residue: 0.2502 time to fit residues: 161.0039 Evaluate side-chains 281 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.0670 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 32 GLN ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 78 GLN Z 98 ASN Y 90 GLN ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 246 ASN C 29 ASN C 66 GLN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 263 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 78 GLN E 28 GLN E 30 HIS E 223 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 11787 Z= 0.278 Angle : 0.775 11.702 16038 Z= 0.397 Chirality : 0.046 0.168 1947 Planarity : 0.006 0.058 1998 Dihedral : 7.516 39.982 1650 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer Outliers : 5.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -5.30 (0.15), residues: 1521 helix: -3.18 (0.11), residues: 1059 sheet: None (None), residues: 0 loop : -3.89 (0.22), residues: 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 288 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 49 residues processed: 324 average time/residue: 0.2371 time to fit residues: 107.4907 Evaluate side-chains 294 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 245 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.1015 time to fit residues: 10.9920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 41 GLN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 90 GLN ** Y 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 172 ASN C 32 GLN C 66 GLN C 230 HIS ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 180 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 11787 Z= 0.233 Angle : 0.722 13.485 16038 Z= 0.363 Chirality : 0.045 0.204 1947 Planarity : 0.005 0.052 1998 Dihedral : 6.930 39.450 1650 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -4.41 (0.17), residues: 1521 helix: -2.43 (0.13), residues: 1074 sheet: None (None), residues: 0 loop : -3.81 (0.23), residues: 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 260 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 277 average time/residue: 0.2494 time to fit residues: 96.5483 Evaluate side-chains 262 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 245 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1085 time to fit residues: 5.3324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 0.0070 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN C 71 HIS ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN F 66 GLN ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11787 Z= 0.196 Angle : 0.674 11.501 16038 Z= 0.341 Chirality : 0.043 0.232 1947 Planarity : 0.005 0.052 1998 Dihedral : 6.513 39.626 1650 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.41 % 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: -3.71 (0.19), residues: 1521 helix: -1.90 (0.14), residues: 1077 sheet: None (None), residues: 0 loop : -3.54 (0.23), residues: 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 256 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 274 average time/residue: 0.2428 time to fit residues: 93.7062 Evaluate side-chains 269 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1031 time to fit residues: 6.4696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 11787 Z= 0.203 Angle : 0.676 11.725 16038 Z= 0.338 Chirality : 0.043 0.235 1947 Planarity : 0.005 0.053 1998 Dihedral : 6.267 39.120 1650 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.41 % 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: -3.19 (0.19), residues: 1521 helix: -1.47 (0.15), residues: 1059 sheet: None (None), residues: 0 loop : -3.42 (0.23), residues: 462 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 241 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 256 average time/residue: 0.2438 time to fit residues: 87.9448 Evaluate side-chains 246 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 233 time to evaluate : 1.429 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1034 time to fit residues: 4.1859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN F 32 GLN ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 11787 Z= 0.200 Angle : 0.692 16.098 16038 Z= 0.337 Chirality : 0.043 0.261 1947 Planarity : 0.005 0.054 1998 Dihedral : 6.055 39.323 1650 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.41 % 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: -2.92 (0.20), residues: 1521 helix: -1.29 (0.15), residues: 1074 sheet: None (None), residues: 0 loop : -3.32 (0.24), residues: 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 252 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 265 average time/residue: 0.2457 time to fit residues: 91.7436 Evaluate side-chains 249 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 236 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1044 time to fit residues: 4.2946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN E 246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 11787 Z= 0.218 Angle : 0.688 13.954 16038 Z= 0.338 Chirality : 0.043 0.180 1947 Planarity : 0.005 0.054 1998 Dihedral : 5.931 38.523 1650 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.41 % 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: -2.77 (0.20), residues: 1521 helix: -1.17 (0.15), residues: 1074 sheet: None (None), residues: 0 loop : -3.26 (0.24), residues: 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 245 time to evaluate : 1.405 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 248 average time/residue: 0.2282 time to fit residues: 81.4013 Evaluate side-chains 239 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 230 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1030 time to fit residues: 3.5137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.0870 chunk 43 optimal weight: 0.0980 chunk 28 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN C 66 GLN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 11787 Z= 0.170 Angle : 0.660 12.768 16038 Z= 0.323 Chirality : 0.042 0.166 1947 Planarity : 0.005 0.053 1998 Dihedral : 5.678 37.631 1650 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.41 % 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: -2.61 (0.20), residues: 1521 helix: -1.03 (0.16), residues: 1080 sheet: None (None), residues: 0 loop : -3.28 (0.24), residues: 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 235 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 243 average time/residue: 0.2260 time to fit residues: 78.6794 Evaluate side-chains 229 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 222 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1040 time to fit residues: 3.0806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0770 chunk 138 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 29 ASN ** Z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 90 GLN ** Y 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN B 172 ASN B 246 ASN ** F 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 11787 Z= 0.294 Angle : 0.741 12.390 16038 Z= 0.361 Chirality : 0.045 0.161 1947 Planarity : 0.005 0.054 1998 Dihedral : 5.872 38.742 1650 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.41 % 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: -2.73 (0.20), residues: 1521 helix: -1.18 (0.15), residues: 1098 sheet: None (None), residues: 0 loop : -3.21 (0.25), residues: 423 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 243 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 249 average time/residue: 0.2417 time to fit residues: 84.9686 Evaluate side-chains 244 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 235 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1032 time to fit residues: 3.5271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 149 optimal weight: 0.7980 chunk 137 optimal weight: 0.1980 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 94 optimal weight: 0.1980 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN B 172 ASN F 32 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 11787 Z= 0.180 Angle : 0.685 11.658 16038 Z= 0.334 Chirality : 0.042 0.160 1947 Planarity : 0.005 0.053 1998 Dihedral : 5.636 36.796 1650 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.41 % 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: -2.56 (0.20), residues: 1521 helix: -0.97 (0.16), residues: 1074 sheet: None (None), residues: 0 loop : -3.32 (0.24), residues: 447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 227 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 229 average time/residue: 0.2430 time to fit residues: 79.4565 Evaluate side-chains 220 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1071 time to fit residues: 2.1478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN F 32 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119160 restraints weight = 16094.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122527 restraints weight = 9227.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124719 restraints weight = 6558.311| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 11787 Z= 0.294 Angle : 0.731 12.057 16038 Z= 0.356 Chirality : 0.045 0.159 1947 Planarity : 0.005 0.053 1998 Dihedral : 5.788 38.007 1650 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.41 % 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: -2.57 (0.20), residues: 1521 helix: -1.02 (0.15), residues: 1083 sheet: None (None), residues: 0 loop : -3.23 (0.25), residues: 438 =============================================================================== Job complete usr+sys time: 2409.32 seconds wall clock time: 44 minutes 22.88 seconds (2662.88 seconds total)