Starting phenix.real_space_refine (version: dev) on Sat Feb 18 15:18:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/02_2023/7ryc_24733_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/02_2023/7ryc_24733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/02_2023/7ryc_24733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/02_2023/7ryc_24733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/02_2023/7ryc_24733_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/02_2023/7ryc_24733_updated.pdb" } resolution = 2.9 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= 0.008 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 67 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D ARG 1015": "NH1" <-> "NH2" Residue "D ARG 1024": "NH1" <-> "NH2" Residue "D ARG 1117": "NH1" <-> "NH2" Residue "D GLU 1120": "OE1" <-> "OE2" Residue "D GLU 1151": "OE1" <-> "OE2" Residue "D GLU 1166": "OE1" <-> "OE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 160": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8277 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 69 Unusual residues: {'NH2': 1} Classifications: {'peptide': 9, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 7} Chain: "O" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2097 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 133 Chain: "D" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1973 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2442 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 108 Chain: "E" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1695 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.14, per 1000 atoms: 0.62 Number of scatterers: 8277 At special positions: 0 Unit cell: (89.4705, 124.407, 130.371, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 Mg 1 11.99 O 1491 8.00 N 1409 7.00 C 5321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.03 Simple disulfide: pdb=" SG CYS O 112 " - pdb=" SG CYS O 187 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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: 2.95 Conformation dependent library (CDL) restraints added in 1.3 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 32.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'O' and resid 36 through 66 removed outlier: 3.740A pdb=" N GLU O 42 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL O 43 " --> pdb=" O ALA O 39 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA O 44 " --> pdb=" O ARG O 40 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS O 47 " --> pdb=" O VAL O 43 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 91 Processing helix chain 'O' and resid 94 through 101 removed outlier: 3.699A pdb=" N ASP O 100 " --> pdb=" O GLN O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 142 removed outlier: 4.007A pdb=" N TYR O 117 " --> pdb=" O ARG O 113 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU O 130 " --> pdb=" O SER O 126 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU O 131 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 167 removed outlier: 4.632A pdb=" N VAL O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 174 removed outlier: 4.210A pdb=" N ILE O 174 " --> pdb=" O GLN O 171 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 208 Processing helix chain 'O' and resid 210 through 234 removed outlier: 4.025A pdb=" N TYR O 220 " --> pdb=" O LEU O 216 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER O 224 " --> pdb=" O TYR O 220 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE O 225 " --> pdb=" O GLY O 221 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP O 228 " --> pdb=" O SER O 224 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU O 231 " --> pdb=" O ILE O 227 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG O 232 " --> pdb=" O TRP O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 272 through 298 removed outlier: 4.224A pdb=" N ILE O 279 " --> pdb=" O LYS O 275 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE O 280 " --> pdb=" O MET O 276 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE O 284 " --> pdb=" O ILE O 280 " (cutoff:3.500A) Proline residue: O 290 - end of helix Processing helix chain 'O' and resid 309 through 315 Processing helix chain 'O' and resid 321 through 331 Proline residue: O 326 - end of helix Processing helix chain 'O' and resid 335 through 344 Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.959A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 33 No H-bonds generated for 'chain 'D' and resid 30 through 33' Processing helix chain 'D' and resid 35 through 43 removed outlier: 3.556A pdb=" N ALA D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 35 through 43' Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 1007 through 1030 removed outlier: 3.849A pdb=" N ALA D1011 " --> pdb=" O ALA D1007 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET D1018 " --> pdb=" O GLU D1014 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE D1019 " --> pdb=" O ARG D1015 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP D1020 " --> pdb=" O SER D1016 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS D1021 " --> pdb=" O LYS D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1046 through 1048 No H-bonds generated for 'chain 'D' and resid 1046 through 1048' Processing helix chain 'D' and resid 1096 through 1098 No H-bonds generated for 'chain 'D' and resid 1096 through 1098' Processing helix chain 'D' and resid 1118 through 1129 Processing helix chain 'D' and resid 1146 through 1155 removed outlier: 3.542A pdb=" N ALA D1150 " --> pdb=" O GLN D1146 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D1151 " --> pdb=" O ASP D1147 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1162 No H-bonds generated for 'chain 'D' and resid 1160 through 1162' Processing helix chain 'D' and resid 1165 through 1168 Processing helix chain 'D' and resid 1184 through 1203 removed outlier: 3.858A pdb=" N PHE D1197 " --> pdb=" O ILE D1193 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D1200 " --> pdb=" O GLU D1196 " (cutoff:3.500A) Processing helix chain 'D' and resid 1224 through 1242 removed outlier: 3.666A pdb=" N PHE D1228 " --> pdb=" O ALA D1224 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D1233 " --> pdb=" O ASN D1229 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN D1237 " --> pdb=" O ASP D1233 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D1240 " --> pdb=" O LEU D1236 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARG D1241 " --> pdb=" O GLN D1237 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU D1242 " --> pdb=" O MET D1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 23 removed outlier: 4.277A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 4.637A pdb=" N ASN C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'O' and resid 175 through 181 removed outlier: 6.768A pdb=" N VAL O 184 " --> pdb=" O VAL O 180 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 1211 through 1215 removed outlier: 7.138A pdb=" N VAL D1139 " --> pdb=" O TYR D1212 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N HIS D1214 " --> pdb=" O VAL D1139 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU D1141 " --> pdb=" O HIS D1214 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA D1105 " --> pdb=" O ARG D1035 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.139A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.844A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.850A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.781A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 262 through 264 removed outlier: 3.518A pdb=" N CYS C 250 " --> pdb=" O TYR C 264 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 294 through 298 removed outlier: 3.902A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 327 through 329 removed outlier: 3.602A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 4 through 6 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.540A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER E 99 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP E 36 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 7.047A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.003A pdb=" N CYS E 159 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE E 212 " --> pdb=" O CYS E 159 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 229 through 231 removed outlier: 3.983A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 903 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: 2.47 Time building geometry restraints manager: 3.23 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: 1850 1.33 - 1.45: 1916 1.45 - 1.58: 4613 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 8455 Sorted by residual: bond pdb=" C TRP O 203 " pdb=" N ILE O 204 " ideal model delta sigma weight residual 1.335 1.257 0.077 1.26e-02 6.30e+03 3.77e+01 bond pdb=" C LEU O 139 " pdb=" N ALA O 140 " ideal model delta sigma weight residual 1.334 1.423 -0.088 1.49e-02 4.50e+03 3.52e+01 bond pdb=" C VAL O 157 " pdb=" N LEU O 158 " ideal model delta sigma weight residual 1.335 1.256 0.079 1.36e-02 5.41e+03 3.35e+01 bond pdb=" C ARG D1117 " pdb=" N LEU D1118 " ideal model delta sigma weight residual 1.335 1.259 0.076 1.36e-02 5.41e+03 3.13e+01 bond pdb=" C LYS O 270 " pdb=" N ILE O 271 " ideal model delta sigma weight residual 1.332 1.257 0.075 1.36e-02 5.41e+03 3.01e+01 ... (remaining 8450 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.54: 207 106.54 - 113.41: 4600 113.41 - 120.29: 3102 120.29 - 127.17: 3529 127.17 - 134.05: 95 Bond angle restraints: 11533 Sorted by residual: angle pdb=" N ILE O 101 " pdb=" CA ILE O 101 " pdb=" C ILE O 101 " ideal model delta sigma weight residual 110.42 105.48 4.94 9.60e-01 1.09e+00 2.65e+01 angle pdb=" O VAL O 157 " pdb=" C VAL O 157 " pdb=" N LEU O 158 " ideal model delta sigma weight residual 121.87 117.12 4.75 9.70e-01 1.06e+00 2.40e+01 angle pdb=" N CYS O 138 " pdb=" CA CYS O 138 " pdb=" C CYS O 138 " ideal model delta sigma weight residual 111.28 116.47 -5.19 1.09e+00 8.42e-01 2.26e+01 angle pdb=" O TRP O 203 " pdb=" C TRP O 203 " pdb=" N ILE O 204 " ideal model delta sigma weight residual 122.07 117.40 4.67 1.03e+00 9.43e-01 2.05e+01 angle pdb=" N ARG O 73 " pdb=" CA ARG O 73 " pdb=" C ARG O 73 " ideal model delta sigma weight residual 112.97 108.37 4.60 1.06e+00 8.90e-01 1.88e+01 ... (remaining 11528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 4411 15.92 - 31.83: 388 31.83 - 47.75: 103 47.75 - 63.66: 23 63.66 - 79.58: 6 Dihedral angle restraints: 4931 sinusoidal: 1668 harmonic: 3263 Sorted by residual: dihedral pdb=" CB CYS O 112 " pdb=" SG CYS O 112 " pdb=" SG CYS O 187 " pdb=" CB CYS O 187 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CA ARG D1032 " pdb=" C ARG D1032 " pdb=" N THR D1033 " pdb=" CA THR D1033 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ARG D1031 " pdb=" C ARG D1031 " pdb=" N ARG D1032 " pdb=" CA ARG D1032 " ideal model delta harmonic sigma weight residual -180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 4928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1014 0.052 - 0.104: 248 0.104 - 0.156: 73 0.156 - 0.208: 16 0.208 - 0.260: 6 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA ILE O 101 " pdb=" N ILE O 101 " pdb=" C ILE O 101 " pdb=" CB ILE O 101 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA LEU C 210 " pdb=" N LEU C 210 " pdb=" C LEU C 210 " pdb=" CB LEU C 210 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1354 not shown) Planarity restraints: 1455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS O 270 " -0.013 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C LYS O 270 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS O 270 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE O 271 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU O 139 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C LEU O 139 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU O 139 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA O 140 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL O 294 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C VAL O 294 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL O 294 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN O 295 " -0.010 2.00e-02 2.50e+03 ... (remaining 1452 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 659 2.74 - 3.28: 7589 3.28 - 3.82: 11922 3.82 - 4.36: 14470 4.36 - 4.90: 25750 Nonbonded interactions: 60390 Sorted by model distance: nonbonded pdb=" O ASP D1233 " pdb=" OD1 ASP D1233 " model vdw 2.198 3.040 nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.278 2.440 nonbonded pdb=" OD1 ASP O 100 " pdb="MG MG O 401 " model vdw 2.281 2.170 nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.296 2.520 nonbonded pdb=" O GLN D1119 " pdb=" ND2 ASN D1123 " model vdw 2.312 2.520 ... (remaining 60385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 55 5.16 5 C 5321 2.51 5 N 1409 2.21 5 O 1491 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 7.420 Check model and map are aligned: 0.130 Process input model: 24.850 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.006 0.088 8455 Z= 0.414 Angle : 0.864 8.554 11533 Z= 0.575 Chirality : 0.053 0.260 1357 Planarity : 0.004 0.044 1455 Dihedral : 13.762 79.578 2808 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.22), residues: 1099 helix: -1.76 (0.25), residues: 346 sheet: -1.30 (0.31), residues: 247 loop : -2.44 (0.22), residues: 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 0.936 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 143 average time/residue: 1.3198 time to fit residues: 199.9516 Evaluate side-chains 94 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.1767 time to fit residues: 2.6326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 0.0670 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 GLN O 171 GLN D 59 ASN D1101 ASN C 183 HIS E 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8455 Z= 0.178 Angle : 0.570 8.786 11533 Z= 0.297 Chirality : 0.042 0.154 1357 Planarity : 0.004 0.034 1455 Dihedral : 4.371 22.942 1194 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.24), residues: 1099 helix: -0.42 (0.28), residues: 346 sheet: -0.74 (0.30), residues: 285 loop : -2.10 (0.25), residues: 468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 1.139 Fit side-chains outliers start: 17 outliers final: 3 residues processed: 115 average time/residue: 1.3188 time to fit residues: 161.3159 Evaluate side-chains 106 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.6062 time to fit residues: 2.6715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 89 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 295 GLN D 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 8455 Z= 0.137 Angle : 0.511 9.415 11533 Z= 0.264 Chirality : 0.040 0.143 1357 Planarity : 0.003 0.028 1455 Dihedral : 4.019 23.891 1194 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.25), residues: 1099 helix: 0.35 (0.29), residues: 346 sheet: -0.37 (0.31), residues: 280 loop : -1.79 (0.26), residues: 473 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 0.982 Fit side-chains outliers start: 23 outliers final: 8 residues processed: 121 average time/residue: 1.3492 time to fit residues: 173.2465 Evaluate side-chains 113 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.1808 time to fit residues: 2.0126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8455 Z= 0.242 Angle : 0.577 7.885 11533 Z= 0.301 Chirality : 0.042 0.142 1357 Planarity : 0.003 0.037 1455 Dihedral : 4.221 18.579 1194 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 4.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1099 helix: 0.34 (0.29), residues: 344 sheet: -0.19 (0.32), residues: 273 loop : -1.74 (0.26), residues: 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 105 time to evaluate : 1.010 Fit side-chains outliers start: 37 outliers final: 17 residues processed: 125 average time/residue: 1.2138 time to fit residues: 161.7199 Evaluate side-chains 119 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 9 average time/residue: 0.8120 time to fit residues: 9.2930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 96 optimal weight: 0.3980 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 GLN D 59 ASN D1080 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 8455 Z= 0.163 Angle : 0.517 7.180 11533 Z= 0.269 Chirality : 0.041 0.138 1357 Planarity : 0.003 0.031 1455 Dihedral : 4.002 23.268 1194 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1099 helix: 0.74 (0.29), residues: 342 sheet: -0.21 (0.30), residues: 300 loop : -1.58 (0.27), residues: 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.854 Fit side-chains outliers start: 26 outliers final: 11 residues processed: 122 average time/residue: 1.3242 time to fit residues: 171.3274 Evaluate side-chains 116 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.1902 time to fit residues: 2.1232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 0.0570 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 8455 Z= 0.162 Angle : 0.524 10.185 11533 Z= 0.270 Chirality : 0.040 0.136 1357 Planarity : 0.003 0.031 1455 Dihedral : 3.920 21.597 1194 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 3.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1099 helix: 0.94 (0.29), residues: 349 sheet: -0.05 (0.31), residues: 282 loop : -1.40 (0.27), residues: 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 1.154 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 130 average time/residue: 1.3010 time to fit residues: 179.9671 Evaluate side-chains 117 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.1598 time to fit residues: 2.5424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8455 Z= 0.185 Angle : 0.540 8.491 11533 Z= 0.279 Chirality : 0.041 0.135 1357 Planarity : 0.003 0.032 1455 Dihedral : 3.935 20.879 1194 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1099 helix: 0.98 (0.29), residues: 353 sheet: -0.09 (0.31), residues: 294 loop : -1.37 (0.27), residues: 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.942 Fit side-chains outliers start: 28 outliers final: 11 residues processed: 123 average time/residue: 1.3329 time to fit residues: 174.9929 Evaluate side-chains 116 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1586 time to fit residues: 1.7862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8455 Z= 0.182 Angle : 0.541 8.355 11533 Z= 0.280 Chirality : 0.041 0.136 1357 Planarity : 0.003 0.031 1455 Dihedral : 3.911 21.457 1194 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1099 helix: 1.17 (0.29), residues: 349 sheet: -0.01 (0.31), residues: 284 loop : -1.30 (0.27), residues: 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.015 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 121 average time/residue: 1.3367 time to fit residues: 172.1874 Evaluate side-chains 114 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1902 time to fit residues: 2.0620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.0040 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 64 optimal weight: 0.3980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8455 Z= 0.138 Angle : 0.509 8.220 11533 Z= 0.262 Chirality : 0.040 0.135 1357 Planarity : 0.003 0.028 1455 Dihedral : 3.738 24.152 1194 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1099 helix: 1.40 (0.29), residues: 348 sheet: 0.10 (0.32), residues: 284 loop : -1.23 (0.27), residues: 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.044 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 120 average time/residue: 1.3883 time to fit residues: 176.5970 Evaluate side-chains 116 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.2019 time to fit residues: 1.5461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.0040 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 8455 Z= 0.159 Angle : 0.545 10.516 11533 Z= 0.279 Chirality : 0.040 0.134 1357 Planarity : 0.003 0.033 1455 Dihedral : 3.724 22.170 1194 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1099 helix: 1.46 (0.29), residues: 348 sheet: 0.04 (0.31), residues: 294 loop : -1.17 (0.28), residues: 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.963 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 115 average time/residue: 1.3289 time to fit residues: 162.0820 Evaluate side-chains 117 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.2077 time to fit residues: 1.5567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.0770 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.0770 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.0020 overall best weight: 0.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.134416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.112845 restraints weight = 14386.647| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.97 r_work: 0.3387 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 8455 Z= 0.131 Angle : 0.515 10.226 11533 Z= 0.262 Chirality : 0.040 0.137 1357 Planarity : 0.003 0.031 1455 Dihedral : 3.585 24.812 1194 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1099 helix: 1.67 (0.29), residues: 347 sheet: 0.26 (0.32), residues: 282 loop : -1.17 (0.27), residues: 470 =============================================================================== Job complete usr+sys time: 3453.81 seconds wall clock time: 62 minutes 6.70 seconds (3726.70 seconds total)