Starting phenix.real_space_refine on Tue Feb 13 19:30:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9c_30311/02_2024/7c9c_30311_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9c_30311/02_2024/7c9c_30311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9c_30311/02_2024/7c9c_30311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9c_30311/02_2024/7c9c_30311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9c_30311/02_2024/7c9c_30311_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9c_30311/02_2024/7c9c_30311_updated.pdb" } resolution = 3.33 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 18 5.49 5 S 33 5.16 5 C 4656 2.51 5 N 1293 2.21 5 O 1449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C GLU 323": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7452 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.47, per 1000 atoms: 0.60 Number of scatterers: 7452 At special positions: 0 Unit cell: (72.24, 113.4, 112.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 33 16.00 P 18 15.00 O 1449 8.00 N 1293 7.00 C 4656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.4 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 9 sheets defined 39.9% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.560A pdb=" N LEU A 27 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 28 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 41 removed outlier: 3.650A pdb=" N LYS A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.512A pdb=" N GLN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 removed outlier: 4.242A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 removed outlier: 3.950A pdb=" N ASN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.535A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 144 removed outlier: 3.609A pdb=" N CYS A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLN A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 167 through 174 removed outlier: 3.743A pdb=" N ARG A 171 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 173 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.914A pdb=" N ASN A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 4.152A pdb=" N LEU A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 239 through 259 removed outlier: 3.571A pdb=" N ALA A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'B' and resid 24 through 30 removed outlier: 3.560A pdb=" N LEU B 27 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 28 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 removed outlier: 3.649A pdb=" N LYS B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.514A pdb=" N GLN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 60 No H-bonds generated for 'chain 'B' and resid 57 through 60' Processing helix chain 'B' and resid 71 through 78 removed outlier: 3.949A pdb=" N ASN B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.536A pdb=" N LEU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 removed outlier: 3.609A pdb=" N CYS B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLN B 144 " --> pdb=" O CYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 167 through 174 removed outlier: 3.743A pdb=" N ARG B 171 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 173 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 187 removed outlier: 3.915A pdb=" N ASN B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 4.153A pdb=" N LEU B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 239 through 259 removed outlier: 3.570A pdb=" N ALA B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'C' and resid 24 through 30 removed outlier: 3.560A pdb=" N LEU C 27 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 28 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS C 29 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 41 removed outlier: 3.649A pdb=" N LYS C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 3.513A pdb=" N GLN C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 4.242A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.949A pdb=" N ASN C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.536A pdb=" N LEU C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 144 removed outlier: 3.608A pdb=" N CYS C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLN C 144 " --> pdb=" O CYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 167 through 174 removed outlier: 3.744A pdb=" N ARG C 171 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 173 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 187 removed outlier: 3.914A pdb=" N ASN C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 212 removed outlier: 4.152A pdb=" N LEU C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP C 204 " --> pdb=" O MET C 200 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 239 through 259 removed outlier: 3.570A pdb=" N ALA C 247 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 296 Processing sheet with id= A, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.521A pdb=" N ALA A 313 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 264 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA A 124 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 266 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLY A 126 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN A 268 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 267 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LYS A 155 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 220 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 157 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE A 222 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 159 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 270 through 272 Processing sheet with id= C, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.546A pdb=" N GLY A 334 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.520A pdb=" N ALA B 313 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 264 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA B 124 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 266 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLY B 126 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN B 268 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 267 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LYS B 155 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 220 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 157 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE B 222 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 159 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 270 through 272 Processing sheet with id= F, first strand: chain 'B' and resid 329 through 331 removed outlier: 3.545A pdb=" N GLY B 334 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.521A pdb=" N ALA C 313 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 264 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA C 124 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL C 266 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLY C 126 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN C 268 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 267 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LYS C 155 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 220 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE C 157 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE C 222 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 159 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 270 through 272 Processing sheet with id= I, first strand: chain 'C' and resid 329 through 331 removed outlier: 3.547A pdb=" N GLY C 334 " --> pdb=" O THR C 331 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 492 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: 2.00 Time building geometry restraints manager: 3.22 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: 1654 1.33 - 1.45: 1544 1.45 - 1.57: 4302 1.57 - 1.69: 26 1.69 - 1.81: 57 Bond restraints: 7583 Sorted by residual: bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.544 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.544 0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" O3A ANP C 402 " pdb=" PB ANP C 402 " ideal model delta sigma weight residual 1.700 1.545 0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.682 0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 1.795 1.682 0.113 2.00e-02 2.50e+03 3.20e+01 ... (remaining 7578 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.27: 205 106.27 - 112.83: 4005 112.83 - 119.39: 2318 119.39 - 125.96: 3644 125.96 - 132.52: 78 Bond angle restraints: 10250 Sorted by residual: angle pdb=" PB ANP C 402 " pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 126.95 107.75 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 107.76 19.19 3.00e+00 1.11e-01 4.09e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 107.77 19.18 3.00e+00 1.11e-01 4.09e+01 angle pdb=" C LYS A 79 " pdb=" N LEU A 80 " pdb=" CA LEU A 80 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 angle pdb=" C LYS B 79 " pdb=" N LEU B 80 " pdb=" CA LEU B 80 " ideal model delta sigma weight residual 121.54 128.57 -7.03 1.91e+00 2.74e-01 1.35e+01 ... (remaining 10245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.10: 4251 26.10 - 52.20: 270 52.20 - 78.30: 72 78.30 - 104.40: 21 104.40 - 130.50: 3 Dihedral angle restraints: 4617 sinusoidal: 1992 harmonic: 2625 Sorted by residual: dihedral pdb=" CA GLU A 82 " pdb=" C GLU A 82 " pdb=" N PRO A 83 " pdb=" CA PRO A 83 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA GLU C 82 " pdb=" C GLU C 82 " pdb=" N PRO C 83 " pdb=" CA PRO C 83 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA GLU B 82 " pdb=" C GLU B 82 " pdb=" N PRO B 83 " pdb=" CA PRO B 83 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 4614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 914 0.062 - 0.124: 209 0.124 - 0.186: 25 0.186 - 0.248: 4 0.248 - 0.310: 3 Chirality restraints: 1155 Sorted by residual: chirality pdb=" C3' ANP A 402 " pdb=" C2' ANP A 402 " pdb=" C4' ANP A 402 " pdb=" O3' ANP A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C3' ANP C 402 " pdb=" C2' ANP C 402 " pdb=" C4' ANP C 402 " pdb=" O3' ANP C 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1152 not shown) Planarity restraints: 1278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 128 " -0.009 2.00e-02 2.50e+03 1.51e-02 4.00e+00 pdb=" CG PHE B 128 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 128 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 128 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 128 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 128 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 128 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 128 " -0.009 2.00e-02 2.50e+03 1.51e-02 4.00e+00 pdb=" CG PHE C 128 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 128 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE C 128 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 128 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 128 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 128 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 128 " 0.008 2.00e-02 2.50e+03 1.49e-02 3.88e+00 pdb=" CG PHE A 128 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 128 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 128 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 128 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 128 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 128 " -0.001 2.00e-02 2.50e+03 ... (remaining 1275 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 4 1.97 - 2.70: 237 2.70 - 3.43: 9314 3.43 - 4.17: 16898 4.17 - 4.90: 31397 Nonbonded interactions: 57850 Sorted by model distance: nonbonded pdb=" NH1 ARG C 56 " pdb=" OD1 ASP C 71 " model vdw 1.232 2.520 nonbonded pdb="CA CA B 401 " pdb=" O1G ANP B 402 " model vdw 1.678 2.510 nonbonded pdb="CA CA C 401 " pdb=" O1G ANP C 402 " model vdw 1.763 2.510 nonbonded pdb=" CZ ARG C 56 " pdb=" OD1 ASP C 71 " model vdw 1.789 3.270 nonbonded pdb="CA CA A 401 " pdb=" O1G ANP A 402 " model vdw 1.989 2.510 ... (remaining 57845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.080 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 23.900 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.009 0.156 7583 Z= 0.524 Angle : 1.035 19.200 10250 Z= 0.529 Chirality : 0.056 0.310 1155 Planarity : 0.005 0.041 1278 Dihedral : 19.223 130.497 2931 Min Nonbonded Distance : 1.232 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.79 % Allowed : 6.98 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.45 (0.20), residues: 912 helix: -5.12 (0.06), residues: 351 sheet: -1.95 (0.38), residues: 156 loop : -2.68 (0.24), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 181 PHE 0.033 0.003 PHE C 128 TYR 0.014 0.002 TYR A 316 ARG 0.005 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 171 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7771 (p0) cc_final: 0.7493 (m-30) REVERT: A 252 ARG cc_start: 0.8046 (tpt-90) cc_final: 0.7747 (ttt90) REVERT: B 41 LYS cc_start: 0.6961 (mttt) cc_final: 0.6394 (mttm) REVERT: B 171 ARG cc_start: 0.7424 (tpt170) cc_final: 0.7139 (mtt90) REVERT: C 36 ASP cc_start: 0.6220 (m-30) cc_final: 0.6009 (m-30) REVERT: C 41 LYS cc_start: 0.6410 (mttt) cc_final: 0.5726 (tptt) REVERT: C 285 LYS cc_start: 0.8990 (mttt) cc_final: 0.8372 (mmmt) outliers start: 6 outliers final: 3 residues processed: 177 average time/residue: 0.2882 time to fit residues: 62.5546 Evaluate side-chains 116 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 22 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 78 ASN A 199 GLN A 248 GLN B 61 ASN B 78 ASN B 199 GLN C 61 ASN C 78 ASN C 187 ASN C 199 GLN C 243 GLN C 248 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7583 Z= 0.224 Angle : 0.554 6.991 10250 Z= 0.286 Chirality : 0.043 0.137 1155 Planarity : 0.005 0.076 1278 Dihedral : 15.510 152.097 1184 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.79 % Allowed : 13.31 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.76 (0.22), residues: 912 helix: -4.00 (0.14), residues: 390 sheet: -1.94 (0.35), residues: 189 loop : -2.44 (0.29), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 181 PHE 0.019 0.001 PHE A 128 TYR 0.008 0.001 TYR C 316 ARG 0.009 0.001 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 41 LYS cc_start: 0.6963 (mttt) cc_final: 0.6284 (mttm) REVERT: B 56 ARG cc_start: 0.7227 (mtt180) cc_final: 0.6819 (mtp-110) REVERT: B 168 ASP cc_start: 0.7743 (p0) cc_final: 0.7515 (m-30) REVERT: B 171 ARG cc_start: 0.7290 (tpt170) cc_final: 0.6971 (mtt-85) REVERT: C 41 LYS cc_start: 0.6601 (mttt) cc_final: 0.6093 (tptt) REVERT: C 285 LYS cc_start: 0.8951 (mttt) cc_final: 0.8282 (mmmt) outliers start: 6 outliers final: 4 residues processed: 117 average time/residue: 0.2594 time to fit residues: 38.6946 Evaluate side-chains 100 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 57 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.8501 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7583 Z= 0.225 Angle : 0.517 6.362 10250 Z= 0.271 Chirality : 0.042 0.145 1155 Planarity : 0.005 0.111 1278 Dihedral : 14.699 160.972 1173 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.37 % Allowed : 13.04 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.88 (0.24), residues: 912 helix: -3.17 (0.19), residues: 393 sheet: -1.52 (0.37), residues: 189 loop : -2.08 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 181 PHE 0.017 0.001 PHE A 128 TYR 0.017 0.001 TYR B 316 ARG 0.015 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 102 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8521 (t) REVERT: A 241 GLU cc_start: 0.7647 (tt0) cc_final: 0.7335 (tt0) REVERT: A 321 MET cc_start: 0.8510 (mmm) cc_final: 0.8303 (mmp) REVERT: B 41 LYS cc_start: 0.6940 (mttt) cc_final: 0.6242 (mttm) REVERT: B 52 GLN cc_start: 0.8658 (tt0) cc_final: 0.8455 (tt0) REVERT: B 171 ARG cc_start: 0.7282 (tpt170) cc_final: 0.6972 (mtt180) REVERT: B 186 ASP cc_start: 0.7838 (m-30) cc_final: 0.7584 (m-30) REVERT: B 273 ASP cc_start: 0.8217 (t0) cc_final: 0.8001 (t0) REVERT: C 41 LYS cc_start: 0.6694 (mttt) cc_final: 0.6138 (tptt) REVERT: C 96 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8860 (mttp) REVERT: C 102 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.9029 (t) REVERT: C 285 LYS cc_start: 0.8946 (mttt) cc_final: 0.8335 (mmmt) outliers start: 18 outliers final: 7 residues processed: 112 average time/residue: 0.2570 time to fit residues: 36.7535 Evaluate side-chains 107 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.0570 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7583 Z= 0.135 Angle : 0.447 6.957 10250 Z= 0.234 Chirality : 0.041 0.126 1155 Planarity : 0.005 0.116 1278 Dihedral : 14.497 166.686 1173 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.50 % Allowed : 13.31 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.22 (0.25), residues: 912 helix: -2.54 (0.22), residues: 393 sheet: -1.27 (0.37), residues: 189 loop : -1.81 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 181 PHE 0.014 0.001 PHE A 128 TYR 0.007 0.001 TYR B 316 ARG 0.017 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.7617 (tt0) cc_final: 0.7292 (tt0) REVERT: B 41 LYS cc_start: 0.6934 (mttt) cc_final: 0.6249 (mttm) REVERT: B 52 GLN cc_start: 0.8597 (tt0) cc_final: 0.8394 (tt0) REVERT: B 186 ASP cc_start: 0.7889 (m-30) cc_final: 0.7563 (m-30) REVERT: C 41 LYS cc_start: 0.6676 (mttt) cc_final: 0.6134 (tptt) REVERT: C 96 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8849 (mttp) REVERT: C 285 LYS cc_start: 0.8932 (mttt) cc_final: 0.8391 (mmmt) outliers start: 19 outliers final: 8 residues processed: 114 average time/residue: 0.2385 time to fit residues: 35.1906 Evaluate side-chains 114 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 223 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8461 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7583 Z= 0.136 Angle : 0.441 6.155 10250 Z= 0.232 Chirality : 0.040 0.123 1155 Planarity : 0.007 0.178 1278 Dihedral : 14.561 173.423 1173 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.50 % Allowed : 13.57 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.51 (0.26), residues: 912 helix: -1.87 (0.24), residues: 387 sheet: -0.59 (0.40), residues: 162 loop : -1.74 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 181 PHE 0.012 0.001 PHE A 128 TYR 0.007 0.001 TYR B 316 ARG 0.017 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.7660 (tt0) cc_final: 0.7360 (tt0) REVERT: B 41 LYS cc_start: 0.6945 (mttt) cc_final: 0.6259 (mttm) REVERT: B 52 GLN cc_start: 0.8584 (tt0) cc_final: 0.8376 (tt0) REVERT: B 80 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.7004 (mm) REVERT: B 171 ARG cc_start: 0.7202 (tpt170) cc_final: 0.6906 (mtt-85) REVERT: B 186 ASP cc_start: 0.7966 (m-30) cc_final: 0.7511 (m-30) REVERT: B 223 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.7019 (t0) REVERT: B 273 ASP cc_start: 0.8301 (t0) cc_final: 0.8086 (t0) REVERT: C 96 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8804 (mttp) REVERT: C 285 LYS cc_start: 0.9009 (mttt) cc_final: 0.8312 (mmmt) outliers start: 19 outliers final: 9 residues processed: 123 average time/residue: 0.2189 time to fit residues: 35.3868 Evaluate side-chains 114 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 73 optimal weight: 0.0170 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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: 0.8467 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7583 Z= 0.142 Angle : 0.433 6.008 10250 Z= 0.228 Chirality : 0.041 0.123 1155 Planarity : 0.005 0.139 1278 Dihedral : 14.382 173.854 1173 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.37 % Allowed : 14.36 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.26 (0.27), residues: 912 helix: -1.46 (0.25), residues: 387 sheet: -1.07 (0.37), residues: 195 loop : -1.53 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 181 PHE 0.013 0.001 PHE A 128 TYR 0.006 0.001 TYR B 316 ARG 0.015 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.769 Fit side-chains REVERT: A 241 GLU cc_start: 0.7635 (tt0) cc_final: 0.7296 (tt0) REVERT: B 41 LYS cc_start: 0.6955 (mttt) cc_final: 0.6264 (mttm) REVERT: B 52 GLN cc_start: 0.8579 (tt0) cc_final: 0.8346 (tt0) REVERT: B 73 ILE cc_start: 0.8705 (mt) cc_final: 0.8452 (mp) REVERT: B 80 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.7030 (mm) REVERT: B 171 ARG cc_start: 0.7135 (tpt170) cc_final: 0.6838 (mtt-85) REVERT: B 186 ASP cc_start: 0.8003 (m-30) cc_final: 0.7662 (m-30) REVERT: B 223 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7062 (t0) REVERT: B 273 ASP cc_start: 0.8297 (t0) cc_final: 0.8096 (t0) REVERT: C 41 LYS cc_start: 0.6636 (mttt) cc_final: 0.6136 (tptt) REVERT: C 96 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8796 (mttp) REVERT: C 102 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8704 (t) REVERT: C 285 LYS cc_start: 0.9026 (mttt) cc_final: 0.8294 (mmmt) outliers start: 18 outliers final: 12 residues processed: 119 average time/residue: 0.2462 time to fit residues: 37.5991 Evaluate side-chains 119 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8472 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7583 Z= 0.152 Angle : 0.436 5.897 10250 Z= 0.229 Chirality : 0.041 0.125 1155 Planarity : 0.006 0.133 1278 Dihedral : 14.133 166.218 1173 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.24 % Allowed : 15.15 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.27), residues: 912 helix: -1.24 (0.26), residues: 399 sheet: -0.14 (0.40), residues: 156 loop : -1.86 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 181 PHE 0.012 0.001 PHE A 128 TYR 0.007 0.001 TYR B 316 ARG 0.019 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.7660 (tt0) cc_final: 0.7365 (tt0) REVERT: B 41 LYS cc_start: 0.6960 (mttt) cc_final: 0.6237 (mttm) REVERT: B 73 ILE cc_start: 0.8691 (mt) cc_final: 0.8428 (mp) REVERT: B 171 ARG cc_start: 0.7044 (tpt170) cc_final: 0.6685 (mtt180) REVERT: B 223 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.7048 (t0) REVERT: B 273 ASP cc_start: 0.8290 (t0) cc_final: 0.8063 (t0) REVERT: C 41 LYS cc_start: 0.6657 (mttt) cc_final: 0.6158 (tptt) REVERT: C 96 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8771 (mttp) REVERT: C 102 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8685 (t) REVERT: C 285 LYS cc_start: 0.9033 (mttt) cc_final: 0.8337 (mmmt) outliers start: 17 outliers final: 11 residues processed: 117 average time/residue: 0.2511 time to fit residues: 37.7347 Evaluate side-chains 119 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.0470 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.0670 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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: 0.8452 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7583 Z= 0.117 Angle : 0.422 5.853 10250 Z= 0.222 Chirality : 0.041 0.155 1155 Planarity : 0.005 0.111 1278 Dihedral : 13.734 167.107 1173 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.11 % Allowed : 15.81 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.78 (0.27), residues: 912 helix: -0.95 (0.26), residues: 405 sheet: -0.20 (0.40), residues: 162 loop : -1.78 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 181 PHE 0.012 0.001 PHE A 128 TYR 0.005 0.001 TYR B 91 ARG 0.013 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.6770 (mtp-110) cc_final: 0.6545 (mtt-85) REVERT: A 241 GLU cc_start: 0.7638 (tt0) cc_final: 0.7347 (tt0) REVERT: B 41 LYS cc_start: 0.6944 (mttt) cc_final: 0.6237 (mttm) REVERT: B 73 ILE cc_start: 0.8687 (mt) cc_final: 0.8422 (mp) REVERT: B 171 ARG cc_start: 0.6922 (tpt170) cc_final: 0.6583 (mtt-85) REVERT: B 186 ASP cc_start: 0.8020 (m-30) cc_final: 0.7671 (m-30) REVERT: B 223 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.7056 (t0) REVERT: C 96 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8751 (mttp) REVERT: C 102 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8626 (t) REVERT: C 285 LYS cc_start: 0.9023 (mttt) cc_final: 0.8331 (mmmt) outliers start: 16 outliers final: 11 residues processed: 120 average time/residue: 0.2500 time to fit residues: 38.7968 Evaluate side-chains 117 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 223 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 35 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8477 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7583 Z= 0.160 Angle : 0.442 5.576 10250 Z= 0.232 Chirality : 0.041 0.141 1155 Planarity : 0.005 0.113 1278 Dihedral : 13.791 166.982 1173 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.50 % Allowed : 15.55 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.27), residues: 912 helix: -0.80 (0.27), residues: 402 sheet: 0.01 (0.41), residues: 156 loop : -1.80 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 181 PHE 0.012 0.001 PHE A 108 TYR 0.007 0.001 TYR C 316 ARG 0.014 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.891 Fit side-chains REVERT: A 119 MET cc_start: 0.8700 (mtp) cc_final: 0.8496 (mtm) REVERT: A 241 GLU cc_start: 0.7700 (tt0) cc_final: 0.7401 (tt0) REVERT: B 41 LYS cc_start: 0.6974 (mttt) cc_final: 0.6279 (mttm) REVERT: B 73 ILE cc_start: 0.8681 (mt) cc_final: 0.8411 (mp) REVERT: B 171 ARG cc_start: 0.6981 (tpt170) cc_final: 0.6606 (mtt-85) REVERT: B 186 ASP cc_start: 0.8002 (m-30) cc_final: 0.7638 (m-30) REVERT: B 223 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.7063 (t0) REVERT: C 41 LYS cc_start: 0.6652 (mttt) cc_final: 0.6182 (tptt) REVERT: C 102 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8667 (t) REVERT: C 285 LYS cc_start: 0.9052 (mttt) cc_final: 0.8337 (mmmt) outliers start: 19 outliers final: 14 residues processed: 119 average time/residue: 0.2354 time to fit residues: 36.3924 Evaluate side-chains 120 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8488 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7583 Z= 0.173 Angle : 0.448 5.796 10250 Z= 0.236 Chirality : 0.042 0.140 1155 Planarity : 0.006 0.118 1278 Dihedral : 13.825 167.394 1173 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.11 % Allowed : 15.81 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.66 (0.28), residues: 912 helix: -0.77 (0.27), residues: 405 sheet: -0.52 (0.39), residues: 183 loop : -1.69 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 291 PHE 0.013 0.001 PHE A 108 TYR 0.007 0.001 TYR C 316 ARG 0.014 0.001 ARG B 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.871 Fit side-chains REVERT: A 241 GLU cc_start: 0.7720 (tt0) cc_final: 0.7414 (tt0) REVERT: B 41 LYS cc_start: 0.6994 (mttt) cc_final: 0.6306 (mttm) REVERT: B 73 ILE cc_start: 0.8675 (mt) cc_final: 0.8400 (mp) REVERT: B 186 ASP cc_start: 0.8004 (m-30) cc_final: 0.7618 (m-30) REVERT: B 223 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7062 (t0) REVERT: C 41 LYS cc_start: 0.6640 (mttt) cc_final: 0.6202 (tptt) REVERT: C 102 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8651 (t) REVERT: C 285 LYS cc_start: 0.9064 (mttt) cc_final: 0.8287 (mmmt) outliers start: 16 outliers final: 14 residues processed: 115 average time/residue: 0.2553 time to fit residues: 39.0329 Evaluate side-chains 118 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.127969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.093212 restraints weight = 9150.470| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.89 r_work: 0.2755 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7583 Z= 0.185 Angle : 0.460 5.719 10250 Z= 0.242 Chirality : 0.042 0.138 1155 Planarity : 0.006 0.116 1278 Dihedral : 13.889 168.265 1173 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.24 % Allowed : 16.07 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.28), residues: 912 helix: -0.73 (0.27), residues: 405 sheet: -0.52 (0.39), residues: 183 loop : -1.66 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 291 PHE 0.013 0.001 PHE A 108 TYR 0.008 0.001 TYR C 316 ARG 0.014 0.001 ARG B 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.07 seconds wall clock time: 36 minutes 51.99 seconds (2211.99 seconds total)