Starting phenix.real_space_refine on Mon Mar 11 13:16:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/03_2024/7ryc_24733_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/03_2024/7ryc_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_24733/03_2024/7ryc_24733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/03_2024/7ryc_24733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/03_2024/7ryc_24733_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryc_24733/03_2024/7ryc_24733_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.79, per 1000 atoms: 0.58 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 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: 1.60 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: 2.32 Time building geometry restraints manager: 3.18 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 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: 2.850 Set stop_for_unknowns flag: 0.010 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: 7.070 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 24.770 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 % Allowed : 13.50 % Favored : 86.12 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 36 HIS 0.006 0.001 HIS E 35 PHE 0.018 0.002 PHE C 235 TYR 0.018 0.002 TYR L 2 ARG 0.002 0.000 ARG O 104 *********************** 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 : 0.870 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.5538 (mttt) cc_final: 0.5282 (tmmt) REVERT: D 1018 MET cc_start: 0.6654 (mtp) cc_final: 0.6424 (mtt) REVERT: C 154 ASP cc_start: 0.7708 (m-30) cc_final: 0.7445 (m-30) REVERT: C 188 MET cc_start: 0.8859 (mmp) cc_final: 0.8581 (mmm) REVERT: C 258 ASP cc_start: 0.7636 (t0) cc_final: 0.7231 (t0) outliers start: 3 outliers final: 2 residues processed: 143 average time/residue: 1.3007 time to fit residues: 197.1553 Evaluate side-chains 96 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 296 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.5980 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: 0.6918 ------------------------------------------------------------------------------- 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 176 GLN C 183 HIS E 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8455 Z= 0.196 Angle : 0.586 8.935 11533 Z= 0.305 Chirality : 0.042 0.154 1357 Planarity : 0.004 0.036 1455 Dihedral : 4.841 53.484 1198 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.00 % Allowed : 18.50 % Favored : 79.50 % 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: -1.85 (0.24), residues: 1099 helix: -0.42 (0.28), residues: 343 sheet: -0.69 (0.30), residues: 277 loop : -2.12 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 36 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.002 PHE C 151 TYR 0.011 0.001 TYR O 128 ARG 0.004 0.000 ARG C 49 *********************** 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 126 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.5567 (mttt) cc_final: 0.5235 (tmmt) REVERT: D 1018 MET cc_start: 0.6587 (mtp) cc_final: 0.6268 (mtt) REVERT: D 1244 ASN cc_start: 0.8195 (t0) cc_final: 0.7869 (t0) REVERT: C 154 ASP cc_start: 0.7709 (m-30) cc_final: 0.7432 (m-30) REVERT: C 188 MET cc_start: 0.8866 (mmp) cc_final: 0.8539 (mmm) REVERT: E 69 THR cc_start: 0.6103 (OUTLIER) cc_final: 0.5895 (m) outliers start: 16 outliers final: 5 residues processed: 118 average time/residue: 1.2996 time to fit residues: 163.2099 Evaluate side-chains 111 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1201 SER Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain E residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 0.0040 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 100 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.4570 ------------------------------------------------------------------------------- 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: 0.7365 moved from start: 0.1647 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= 0.150 Angle : 0.525 9.494 11533 Z= 0.271 Chirality : 0.041 0.146 1357 Planarity : 0.003 0.030 1455 Dihedral : 4.300 47.318 1195 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.12 % Allowed : 19.00 % Favored : 77.88 % 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: -1.16 (0.25), residues: 1099 helix: 0.31 (0.29), residues: 343 sheet: -0.41 (0.31), residues: 280 loop : -1.79 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 36 HIS 0.003 0.001 HIS E 35 PHE 0.009 0.001 PHE O 76 TYR 0.017 0.001 TYR L 2 ARG 0.006 0.000 ARG C 137 *********************** 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 135 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: O 206 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8054 (mp) REVERT: D 22 GLU cc_start: 0.6206 (tt0) cc_final: 0.5978 (tt0) REVERT: D 29 LYS cc_start: 0.5529 (mttt) cc_final: 0.5176 (ttmt) REVERT: C 154 ASP cc_start: 0.7685 (m-30) cc_final: 0.7425 (m-30) REVERT: C 226 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: C 258 ASP cc_start: 0.7413 (t0) cc_final: 0.6968 (t0) REVERT: E 87 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7591 (mtp180) outliers start: 25 outliers final: 8 residues processed: 121 average time/residue: 1.2772 time to fit residues: 163.9663 Evaluate side-chains 115 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1201 SER Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain E residue 87 ARG 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: 0.9980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 0.0170 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- 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 C 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1839 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= 0.164 Angle : 0.522 7.499 11533 Z= 0.271 Chirality : 0.041 0.141 1357 Planarity : 0.003 0.029 1455 Dihedral : 4.224 47.525 1195 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.88 % Allowed : 19.25 % Favored : 76.88 % 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: -0.83 (0.25), residues: 1099 helix: 0.61 (0.29), residues: 345 sheet: -0.23 (0.31), residues: 292 loop : -1.63 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 36 HIS 0.004 0.001 HIS C 225 PHE 0.012 0.001 PHE O 76 TYR 0.014 0.001 TYR L 2 ARG 0.005 0.000 ARG C 137 *********************** 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 144 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 0.906 Fit side-chains REVERT: D 22 GLU cc_start: 0.6180 (tt0) cc_final: 0.5939 (tt0) REVERT: D 29 LYS cc_start: 0.5728 (mttt) cc_final: 0.5289 (tmmt) REVERT: D 1018 MET cc_start: 0.6832 (mtp) cc_final: 0.6341 (mtt) REVERT: D 1118 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7572 (mm) REVERT: C 154 ASP cc_start: 0.7698 (m-30) cc_final: 0.7434 (m-30) REVERT: C 226 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: C 258 ASP cc_start: 0.7472 (t0) cc_final: 0.7007 (t0) REVERT: E 87 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7571 (mtp180) REVERT: E 158 SER cc_start: 0.7492 (t) cc_final: 0.7272 (m) outliers start: 31 outliers final: 12 residues processed: 128 average time/residue: 1.1883 time to fit residues: 161.8896 Evaluate side-chains 121 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1118 LEU Chi-restraints excluded: chain D residue 1201 SER Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 186 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.0070 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.0270 chunk 21 optimal weight: 2.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN D1080 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1902 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= 0.238 Angle : 0.576 10.056 11533 Z= 0.300 Chirality : 0.042 0.139 1357 Planarity : 0.003 0.037 1455 Dihedral : 4.367 46.571 1195 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.00 % Allowed : 19.12 % Favored : 76.88 % 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: -0.87 (0.25), residues: 1099 helix: 0.50 (0.29), residues: 343 sheet: -0.15 (0.32), residues: 275 loop : -1.62 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 36 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.002 PHE O 76 TYR 0.015 0.002 TYR L 2 ARG 0.003 0.000 ARG C 137 *********************** 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 135 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6214 (tt0) cc_final: 0.5939 (tt0) REVERT: D 29 LYS cc_start: 0.5635 (mttt) cc_final: 0.5181 (ttmt) REVERT: D 1118 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7613 (mm) REVERT: C 154 ASP cc_start: 0.7719 (m-30) cc_final: 0.7445 (m-30) REVERT: C 226 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: C 258 ASP cc_start: 0.7553 (t0) cc_final: 0.7111 (t0) REVERT: E 87 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7596 (mtp180) REVERT: E 158 SER cc_start: 0.7498 (t) cc_final: 0.7258 (m) outliers start: 32 outliers final: 15 residues processed: 121 average time/residue: 1.2484 time to fit residues: 160.3982 Evaluate side-chains 123 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 204 ILE Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1118 LEU Chi-restraints excluded: chain D residue 1201 SER Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 186 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 0.0470 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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: 0.7374 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8455 Z= 0.154 Angle : 0.517 8.118 11533 Z= 0.266 Chirality : 0.040 0.136 1357 Planarity : 0.003 0.031 1455 Dihedral : 4.132 45.075 1195 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.12 % Allowed : 20.75 % Favored : 76.12 % 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: -0.50 (0.25), residues: 1099 helix: 0.92 (0.29), residues: 345 sheet: -0.05 (0.31), residues: 282 loop : -1.44 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 36 HIS 0.004 0.001 HIS C 225 PHE 0.011 0.001 PHE O 76 TYR 0.018 0.001 TYR L 2 ARG 0.003 0.000 ARG C 137 *********************** 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 133 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6176 (tt0) cc_final: 0.5956 (tt0) REVERT: D 29 LYS cc_start: 0.5664 (mttt) cc_final: 0.5211 (ttmt) REVERT: C 154 ASP cc_start: 0.7697 (m-30) cc_final: 0.7434 (m-30) REVERT: C 226 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: C 258 ASP cc_start: 0.7471 (t0) cc_final: 0.7154 (t0) REVERT: E 38 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7955 (ptt180) REVERT: E 87 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7989 (mtp180) outliers start: 25 outliers final: 10 residues processed: 123 average time/residue: 1.3118 time to fit residues: 171.4326 Evaluate side-chains 119 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 87 ARG 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: 1.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7393 moved from start: 0.2132 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= 0.189 Angle : 0.538 9.914 11533 Z= 0.278 Chirality : 0.041 0.136 1357 Planarity : 0.003 0.032 1455 Dihedral : 4.144 44.552 1195 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.12 % Allowed : 21.00 % Favored : 75.88 % 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: -0.45 (0.25), residues: 1099 helix: 0.95 (0.29), residues: 349 sheet: -0.10 (0.31), residues: 290 loop : -1.38 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 36 HIS 0.004 0.001 HIS C 225 PHE 0.016 0.001 PHE E 68 TYR 0.014 0.001 TYR L 2 ARG 0.007 0.000 ARG C 137 *********************** 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 132 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6185 (tt0) cc_final: 0.5966 (tt0) REVERT: D 29 LYS cc_start: 0.5608 (mttt) cc_final: 0.5250 (mptt) REVERT: D 1018 MET cc_start: 0.6859 (mtp) cc_final: 0.6363 (mtt) REVERT: D 1229 ASN cc_start: 0.7581 (t0) cc_final: 0.7282 (t0) REVERT: C 154 ASP cc_start: 0.7698 (m-30) cc_final: 0.7433 (m-30) REVERT: C 226 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: C 258 ASP cc_start: 0.7518 (t0) cc_final: 0.7232 (t0) REVERT: E 38 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7979 (ptt180) REVERT: E 87 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8000 (mtp180) outliers start: 25 outliers final: 13 residues processed: 124 average time/residue: 1.2410 time to fit residues: 163.5398 Evaluate side-chains 119 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 315 MET Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 87 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 93 optimal weight: 0.0060 chunk 99 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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: 0.7384 moved from start: 0.2214 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= 0.175 Angle : 0.529 9.244 11533 Z= 0.273 Chirality : 0.041 0.139 1357 Planarity : 0.003 0.031 1455 Dihedral : 4.098 44.043 1195 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.62 % Allowed : 22.25 % Favored : 75.12 % 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: -0.35 (0.25), residues: 1099 helix: 1.13 (0.29), residues: 346 sheet: -0.15 (0.30), residues: 302 loop : -1.33 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 36 HIS 0.005 0.001 HIS C 225 PHE 0.014 0.001 PHE E 68 TYR 0.014 0.001 TYR L 2 ARG 0.004 0.000 ARG C 137 *********************** 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 132 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6195 (tt0) cc_final: 0.5968 (tt0) REVERT: D 29 LYS cc_start: 0.5595 (mttt) cc_final: 0.5229 (mptt) REVERT: D 1018 MET cc_start: 0.6823 (mtp) cc_final: 0.6537 (mtt) REVERT: D 1114 ASP cc_start: 0.7044 (t0) cc_final: 0.6472 (p0) REVERT: D 1229 ASN cc_start: 0.7577 (t0) cc_final: 0.7275 (t0) REVERT: C 154 ASP cc_start: 0.7681 (m-30) cc_final: 0.7445 (m-30) REVERT: C 226 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: C 258 ASP cc_start: 0.7530 (t0) cc_final: 0.7293 (t0) REVERT: E 38 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7969 (ptt180) REVERT: E 192 MET cc_start: 0.7838 (ptm) cc_final: 0.7298 (ptm) outliers start: 21 outliers final: 15 residues processed: 126 average time/residue: 1.3888 time to fit residues: 185.9387 Evaluate side-chains 127 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 278 PHE Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1118 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 38 ARG 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: 0.8980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 105 optimal weight: 0.0170 chunk 64 optimal weight: 0.2980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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: 0.7343 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8455 Z= 0.137 Angle : 0.497 9.007 11533 Z= 0.256 Chirality : 0.040 0.146 1357 Planarity : 0.003 0.026 1455 Dihedral : 3.919 43.040 1195 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.38 % Allowed : 23.38 % Favored : 74.25 % 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: -0.10 (0.26), residues: 1099 helix: 1.34 (0.29), residues: 346 sheet: 0.15 (0.32), residues: 286 loop : -1.28 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 36 HIS 0.003 0.001 HIS C 225 PHE 0.011 0.001 PHE E 68 TYR 0.014 0.001 TYR L 2 ARG 0.004 0.000 ARG C 137 *********************** 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 130 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6147 (tt0) cc_final: 0.5926 (tt0) REVERT: D 1018 MET cc_start: 0.6825 (mtp) cc_final: 0.6352 (mtt) REVERT: D 1114 ASP cc_start: 0.6945 (t0) cc_final: 0.6525 (p0) REVERT: D 1229 ASN cc_start: 0.7546 (t0) cc_final: 0.7260 (t0) REVERT: C 154 ASP cc_start: 0.7675 (m-30) cc_final: 0.7429 (m-30) REVERT: C 226 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: E 38 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7913 (ptt180) REVERT: E 192 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7345 (ptm) outliers start: 19 outliers final: 12 residues processed: 126 average time/residue: 1.2757 time to fit residues: 170.3986 Evaluate side-chains 123 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain O residue 278 PHE Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1118 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 192 MET 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: 0.0050 chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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: 0.7349 moved from start: 0.2457 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= 0.152 Angle : 0.515 8.848 11533 Z= 0.266 Chirality : 0.040 0.134 1357 Planarity : 0.003 0.027 1455 Dihedral : 3.910 42.632 1195 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.12 % Allowed : 23.25 % Favored : 74.62 % 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: -0.03 (0.26), residues: 1099 helix: 1.43 (0.29), residues: 346 sheet: 0.08 (0.31), residues: 294 loop : -1.19 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 36 HIS 0.004 0.001 HIS C 225 PHE 0.012 0.001 PHE E 68 TYR 0.013 0.001 TYR L 2 ARG 0.004 0.000 ARG C 137 ********************** 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 126 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 22 GLU cc_start: 0.6152 (tt0) cc_final: 0.5935 (tt0) REVERT: D 1018 MET cc_start: 0.6826 (mtp) cc_final: 0.6559 (mtt) REVERT: D 1114 ASP cc_start: 0.6924 (t0) cc_final: 0.6495 (p0) REVERT: D 1229 ASN cc_start: 0.7534 (t0) cc_final: 0.7328 (t0) REVERT: C 154 ASP cc_start: 0.7674 (m-30) cc_final: 0.7425 (m-30) REVERT: C 226 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: E 38 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7943 (ptt180) outliers start: 17 outliers final: 12 residues processed: 122 average time/residue: 1.3998 time to fit residues: 180.4824 Evaluate side-chains 120 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain D residue 1082 HIS Chi-restraints excluded: chain D residue 1118 LEU Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 186 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108494 restraints weight = 14188.076| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.08 r_work: 0.3307 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2432 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= 0.189 Angle : 0.545 8.688 11533 Z= 0.281 Chirality : 0.041 0.136 1357 Planarity : 0.003 0.030 1455 Dihedral : 4.001 42.540 1195 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.25 % Allowed : 22.62 % Favored : 75.12 % 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: -0.08 (0.26), residues: 1099 helix: 1.42 (0.29), residues: 346 sheet: -0.07 (0.31), residues: 304 loop : -1.18 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 332 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE E 68 TYR 0.014 0.001 TYR L 2 ARG 0.004 0.000 ARG C 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.49 seconds wall clock time: 61 minutes 4.64 seconds (3664.64 seconds total)