Starting phenix.real_space_refine on Sat Apr 6 09:37:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyw_35831/04_2024/8iyw_35831_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyw_35831/04_2024/8iyw_35831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyw_35831/04_2024/8iyw_35831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyw_35831/04_2024/8iyw_35831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyw_35831/04_2024/8iyw_35831_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyw_35831/04_2024/8iyw_35831_updated.pdb" } resolution = 3.45 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= 0.029 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: 5 Type Number sf(0) Gaussians S 43 5.16 5 Cl 1 4.86 5 C 4980 2.51 5 N 1381 2.21 5 O 1444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 14": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ASP 252": "OD1" <-> "OD2" Residue "B ASP 273": "OD1" <-> "OD2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "H ASP 137": "OD1" <-> "OD2" Residue "H ASP 201": "OD1" <-> "OD2" Residue "H TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7849 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1475 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2393 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 119 Chain: "G" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 379 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1655 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 1930 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 617 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 9, 'PHE:plan': 12, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 263 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'OKL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.47, per 1000 atoms: 0.70 Number of scatterers: 7849 At special positions: 0 Unit cell: (87.8, 116.335, 132.797, 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) Cl 1 17.00 S 43 16.00 O 1444 8.00 N 1381 7.00 C 4980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 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: 3.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 34.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'B' and resid 9 through 32 removed outlier: 4.137A pdb=" N LYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 218 removed outlier: 4.794A pdb=" N HIS B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N CYS B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B 216 " --> pdb=" O TRP B 212 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU B 217 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASP B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 297 through 311 removed outlier: 3.871A pdb=" N LYS B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 350 Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 36 removed outlier: 5.677A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'R' and resid 24 through 54 removed outlier: 4.910A pdb=" N LEU R 30 " --> pdb=" O VAL R 27 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.548A pdb=" N LEU R 34 " --> pdb=" O PRO R 31 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY R 41 " --> pdb=" O PHE R 38 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY R 44 " --> pdb=" O GLY R 41 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN R 45 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY R 46 " --> pdb=" O LEU R 43 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE R 54 " --> pdb=" O ILE R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 88 Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 96 through 129 Processing helix chain 'R' and resid 135 through 138 Processing helix chain 'R' and resid 141 through 157 Processing helix chain 'R' and resid 160 through 164 Processing helix chain 'R' and resid 188 through 217 removed outlier: 3.624A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 220 through 222 No H-bonds generated for 'chain 'R' and resid 220 through 222' Processing helix chain 'R' and resid 224 through 261 removed outlier: 4.797A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE R 238 " --> pdb=" O MET R 234 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 266 through 294 removed outlier: 3.583A pdb=" N ARG R 270 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER R 271 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER R 281 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP R 290 " --> pdb=" O SER R 287 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 319 through 324 removed outlier: 7.412A pdb=" N ILE B 265 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N HIS B 322 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 267 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR B 324 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 269 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS B 196 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU B 36 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG B 198 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 38 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE B 200 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLY B 40 " --> pdb=" O PHE B 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.749A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.957A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.737A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.768A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.776A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 284 through 288 removed outlier: 3.508A pdb=" N ALA C 287 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 327 through 329 removed outlier: 3.776A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.772A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.538A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'R' and resid 11 through 13 385 hydrogen bonds defined for protein. 984 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: 2.53 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1407 1.33 - 1.45: 2209 1.45 - 1.58: 4347 1.58 - 1.71: 0 1.71 - 1.83: 55 Bond restraints: 8018 Sorted by residual: bond pdb=" C PHE R 282 " pdb=" N THR R 283 " ideal model delta sigma weight residual 1.335 1.218 0.117 1.38e-02 5.25e+03 7.15e+01 bond pdb=" C VAL R 88 " pdb=" N ARG R 89 " ideal model delta sigma weight residual 1.332 1.400 -0.068 1.52e-02 4.33e+03 2.02e+01 bond pdb=" CA ILE R 98 " pdb=" CB ILE R 98 " ideal model delta sigma weight residual 1.539 1.521 0.018 5.40e-03 3.43e+04 1.07e+01 bond pdb=" N ILE R 212 " pdb=" CA ILE R 212 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.33e-02 5.65e+03 7.98e+00 bond pdb=" N CYS B 287 " pdb=" CA CYS B 287 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.35e-02 5.49e+03 7.75e+00 ... (remaining 8013 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.84: 196 106.84 - 113.67: 4410 113.67 - 120.51: 3070 120.51 - 127.34: 3184 127.34 - 134.17: 94 Bond angle restraints: 10954 Sorted by residual: angle pdb=" CA CYS R 177 " pdb=" C CYS R 177 " pdb=" O CYS R 177 " ideal model delta sigma weight residual 120.40 113.07 7.33 1.05e+00 9.07e-01 4.88e+01 angle pdb=" N TYR R 284 " pdb=" CA TYR R 284 " pdb=" C TYR R 284 " ideal model delta sigma weight residual 111.36 104.59 6.77 1.09e+00 8.42e-01 3.86e+01 angle pdb=" N LEU R 83 " pdb=" CA LEU R 83 " pdb=" C LEU R 83 " ideal model delta sigma weight residual 111.14 104.57 6.57 1.08e+00 8.57e-01 3.70e+01 angle pdb=" C PHE R 282 " pdb=" N THR R 283 " pdb=" CA THR R 283 " ideal model delta sigma weight residual 120.31 111.62 8.69 1.52e+00 4.33e-01 3.27e+01 angle pdb=" C ILE R 116 " pdb=" N PHE R 117 " pdb=" CA PHE R 117 " ideal model delta sigma weight residual 120.65 113.16 7.49 1.32e+00 5.74e-01 3.22e+01 ... (remaining 10949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 4453 23.42 - 46.83: 176 46.83 - 70.25: 18 70.25 - 93.67: 4 93.67 - 117.08: 1 Dihedral angle restraints: 4652 sinusoidal: 1421 harmonic: 3231 Sorted by residual: dihedral pdb=" CA GLN H 82 " pdb=" C GLN H 82 " pdb=" N MET H 83 " pdb=" CA MET H 83 " ideal model delta harmonic sigma weight residual -180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ALA B 7 " pdb=" C ALA B 7 " pdb=" N GLU B 8 " pdb=" CA GLU B 8 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C03 OKL R 401 " pdb=" C04 OKL R 401 " pdb=" C05 OKL R 401 " pdb=" N06 OKL R 401 " ideal model delta sinusoidal sigma weight residual 183.45 66.37 117.08 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 4649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 962 0.050 - 0.100: 245 0.100 - 0.150: 66 0.150 - 0.200: 4 0.200 - 0.250: 4 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA HIS B 196 " pdb=" N HIS B 196 " pdb=" C HIS B 196 " pdb=" CB HIS B 196 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PHE R 105 " pdb=" N PHE R 105 " pdb=" C PHE R 105 " pdb=" CB PHE R 105 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA HIS R 161 " pdb=" N HIS R 161 " pdb=" C HIS R 161 " pdb=" CB HIS R 161 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1278 not shown) Planarity restraints: 1415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 OKL R 401 " -0.012 2.00e-02 2.50e+03 4.04e-02 5.30e+01 pdb=" C07 OKL R 401 " -0.020 2.00e-02 2.50e+03 pdb=" C10 OKL R 401 " 0.006 2.00e-02 2.50e+03 pdb=" C12 OKL R 401 " 0.041 2.00e-02 2.50e+03 pdb=" C13 OKL R 401 " 0.053 2.00e-02 2.50e+03 pdb=" C15 OKL R 401 " 0.015 2.00e-02 2.50e+03 pdb=" N06 OKL R 401 " 0.018 2.00e-02 2.50e+03 pdb=" N09 OKL R 401 " -0.020 2.00e-02 2.50e+03 pdb=" N14 OKL R 401 " 0.054 2.00e-02 2.50e+03 pdb=" N16 OKL R 401 " 0.024 2.00e-02 2.50e+03 pdb=" O08 OKL R 401 " -0.041 2.00e-02 2.50e+03 pdb=" O11 OKL R 401 " -0.016 2.00e-02 2.50e+03 pdb="CL17 OKL R 401 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 177 " -0.018 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C CYS R 177 " 0.066 2.00e-02 2.50e+03 pdb=" O CYS R 177 " -0.025 2.00e-02 2.50e+03 pdb=" N SER R 178 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 210 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.26e+00 pdb=" C LYS B 210 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS B 210 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS B 211 " -0.017 2.00e-02 2.50e+03 ... (remaining 1412 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1789 2.78 - 3.31: 7679 3.31 - 3.84: 12492 3.84 - 4.37: 14213 4.37 - 4.90: 25171 Nonbonded interactions: 61344 Sorted by model distance: nonbonded pdb=" O LYS B 193 " pdb=" ND2 ASN B 194 " model vdw 2.252 2.520 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.260 2.440 nonbonded pdb=" O ARG R 228 " pdb=" OG1 THR R 231 " model vdw 2.278 2.440 nonbonded pdb=" NE ARG H 98 " pdb=" OD1 ASP H 109 " model vdw 2.295 2.520 nonbonded pdb=" O ASN R 17 " pdb=" ND2 ASN R 17 " model vdw 2.298 2.520 ... (remaining 61339 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: 1.310 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: 5.350 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.570 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.005 0.117 8018 Z= 0.303 Angle : 0.837 8.695 10954 Z= 0.518 Chirality : 0.049 0.250 1281 Planarity : 0.005 0.047 1415 Dihedral : 12.733 117.085 2547 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.45 % Allowed : 11.76 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.09 (0.25), residues: 1100 helix: 0.47 (0.27), residues: 353 sheet: 0.06 (0.32), residues: 250 loop : -0.09 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 152 HIS 0.006 0.001 HIS H 35 PHE 0.017 0.002 PHE C 199 TYR 0.025 0.002 TYR R 284 ARG 0.003 0.001 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 0.946 Fit side-chains REVERT: H 68 PHE cc_start: 0.7828 (m-10) cc_final: 0.7427 (m-10) REVERT: R 216 ARG cc_start: 0.7355 (mtt180) cc_final: 0.7067 (mtt-85) outliers start: 10 outliers final: 3 residues processed: 136 average time/residue: 0.2050 time to fit residues: 37.6883 Evaluate side-chains 119 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain R residue 17 ASN Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN B 295 ASN H 113 GLN R 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8018 Z= 0.230 Angle : 0.577 6.329 10954 Z= 0.315 Chirality : 0.044 0.150 1281 Planarity : 0.004 0.039 1415 Dihedral : 7.025 148.948 1192 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.77 % Allowed : 12.19 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.52 (0.25), residues: 1100 helix: 1.27 (0.28), residues: 360 sheet: 0.09 (0.30), residues: 242 loop : -0.09 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 169 HIS 0.005 0.001 HIS R 161 PHE 0.016 0.002 PHE C 235 TYR 0.025 0.002 TYR R 269 ARG 0.004 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: G 44 HIS cc_start: 0.8071 (m-70) cc_final: 0.7794 (m-70) REVERT: G 48 ASP cc_start: 0.7801 (t0) cc_final: 0.7549 (t0) REVERT: R 198 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7732 (m-10) REVERT: R 213 TRP cc_start: 0.8261 (t60) cc_final: 0.7986 (t60) REVERT: R 216 ARG cc_start: 0.7276 (mtt180) cc_final: 0.6865 (mtt-85) outliers start: 26 outliers final: 15 residues processed: 135 average time/residue: 0.1790 time to fit residues: 34.2142 Evaluate side-chains 130 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.0370 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8018 Z= 0.193 Angle : 0.525 6.363 10954 Z= 0.283 Chirality : 0.042 0.153 1281 Planarity : 0.004 0.042 1415 Dihedral : 6.524 136.449 1186 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.92 % Allowed : 12.77 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.67 (0.26), residues: 1100 helix: 1.70 (0.28), residues: 360 sheet: -0.06 (0.30), residues: 246 loop : -0.13 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.004 0.001 HIS C 91 PHE 0.014 0.001 PHE C 199 TYR 0.019 0.001 TYR R 269 ARG 0.003 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 0.880 Fit side-chains REVERT: B 14 GLU cc_start: 0.8521 (tp30) cc_final: 0.8276 (tp30) REVERT: B 336 PHE cc_start: 0.8393 (t80) cc_final: 0.8185 (t80) REVERT: G 48 ASP cc_start: 0.7793 (t0) cc_final: 0.7358 (t0) REVERT: H 231 GLN cc_start: 0.8477 (pp30) cc_final: 0.8209 (pp30) REVERT: R 154 ILE cc_start: 0.8817 (mm) cc_final: 0.8566 (mt) REVERT: R 198 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7674 (m-10) REVERT: R 216 ARG cc_start: 0.7086 (mtt180) cc_final: 0.6854 (mtt-85) outliers start: 27 outliers final: 19 residues processed: 128 average time/residue: 0.1745 time to fit residues: 31.9653 Evaluate side-chains 131 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 255 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 0.0980 chunk 51 optimal weight: 0.0050 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8018 Z= 0.162 Angle : 0.495 6.298 10954 Z= 0.265 Chirality : 0.042 0.164 1281 Planarity : 0.004 0.041 1415 Dihedral : 6.419 141.655 1186 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.63 % Allowed : 14.08 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.79 (0.26), residues: 1100 helix: 1.89 (0.28), residues: 362 sheet: -0.08 (0.30), residues: 246 loop : -0.09 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE C 199 TYR 0.017 0.001 TYR R 269 ARG 0.003 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.918 Fit side-chains REVERT: B 14 GLU cc_start: 0.8446 (tp30) cc_final: 0.8193 (tp30) REVERT: B 254 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8494 (tp) REVERT: C 98 SER cc_start: 0.8304 (m) cc_final: 0.7817 (t) REVERT: G 48 ASP cc_start: 0.7810 (t0) cc_final: 0.7262 (t0) REVERT: H 231 GLN cc_start: 0.8513 (pp30) cc_final: 0.8241 (pp30) REVERT: R 128 ARG cc_start: 0.7528 (mtt180) cc_final: 0.7324 (mtt180) REVERT: R 154 ILE cc_start: 0.8823 (mm) cc_final: 0.8585 (mt) REVERT: R 198 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7669 (m-10) REVERT: R 216 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6912 (mtt-85) outliers start: 25 outliers final: 16 residues processed: 132 average time/residue: 0.1836 time to fit residues: 33.7496 Evaluate side-chains 131 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 220 MET Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 272 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8018 Z= 0.163 Angle : 0.492 6.622 10954 Z= 0.263 Chirality : 0.041 0.158 1281 Planarity : 0.004 0.040 1415 Dihedral : 6.333 141.840 1186 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.77 % Allowed : 15.09 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.80 (0.26), residues: 1100 helix: 2.00 (0.28), residues: 361 sheet: -0.17 (0.30), residues: 247 loop : -0.11 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.001 PHE B 336 TYR 0.018 0.001 TYR B 297 ARG 0.003 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 0.924 Fit side-chains REVERT: B 14 GLU cc_start: 0.8450 (tp30) cc_final: 0.8202 (tp30) REVERT: B 254 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8522 (tp) REVERT: C 98 SER cc_start: 0.8321 (m) cc_final: 0.7829 (t) REVERT: G 44 HIS cc_start: 0.8126 (m170) cc_final: 0.7786 (m170) REVERT: G 48 ASP cc_start: 0.7994 (t0) cc_final: 0.7378 (t0) REVERT: H 183 GLN cc_start: 0.7700 (mt0) cc_final: 0.7386 (tt0) REVERT: H 230 MET cc_start: 0.7913 (ttt) cc_final: 0.7637 (ttt) REVERT: H 231 GLN cc_start: 0.8525 (pp30) cc_final: 0.8223 (pp30) REVERT: R 128 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7337 (mtt180) REVERT: R 154 ILE cc_start: 0.8760 (mm) cc_final: 0.8532 (mt) REVERT: R 198 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7662 (m-10) REVERT: R 216 ARG cc_start: 0.7178 (mtt180) cc_final: 0.6916 (mtt-85) outliers start: 26 outliers final: 19 residues processed: 132 average time/residue: 0.1851 time to fit residues: 34.0365 Evaluate side-chains 133 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 232 PHE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 269 TYR Chi-restraints excluded: chain R residue 272 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 102 optimal weight: 4.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8018 Z= 0.155 Angle : 0.478 6.492 10954 Z= 0.256 Chirality : 0.041 0.185 1281 Planarity : 0.004 0.039 1415 Dihedral : 6.250 142.863 1186 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.92 % Allowed : 15.53 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.86 (0.26), residues: 1100 helix: 2.13 (0.28), residues: 362 sheet: -0.17 (0.30), residues: 250 loop : -0.12 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE B 336 TYR 0.018 0.001 TYR B 297 ARG 0.006 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 0.975 Fit side-chains REVERT: B 14 GLU cc_start: 0.8528 (tp30) cc_final: 0.8250 (tp30) REVERT: B 254 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8500 (tp) REVERT: C 98 SER cc_start: 0.8315 (m) cc_final: 0.7821 (t) REVERT: G 44 HIS cc_start: 0.8172 (m170) cc_final: 0.7899 (m170) REVERT: G 48 ASP cc_start: 0.8055 (t0) cc_final: 0.7421 (t0) REVERT: H 106 SER cc_start: 0.9164 (t) cc_final: 0.8708 (p) REVERT: H 183 GLN cc_start: 0.7712 (mt0) cc_final: 0.7411 (tt0) REVERT: H 231 GLN cc_start: 0.8536 (pp30) cc_final: 0.8224 (pp30) REVERT: R 198 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7647 (m-10) REVERT: R 216 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6894 (mtt-85) outliers start: 27 outliers final: 18 residues processed: 138 average time/residue: 0.1857 time to fit residues: 35.8461 Evaluate side-chains 135 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 269 TYR Chi-restraints excluded: chain R residue 272 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 0.0000 chunk 59 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8018 Z= 0.193 Angle : 0.500 9.214 10954 Z= 0.265 Chirality : 0.042 0.173 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.310 143.810 1186 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.63 % Allowed : 16.40 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.85 (0.26), residues: 1100 helix: 2.19 (0.28), residues: 361 sheet: -0.20 (0.31), residues: 242 loop : -0.18 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS C 91 PHE 0.013 0.001 PHE C 199 TYR 0.020 0.001 TYR B 297 ARG 0.006 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 0.930 Fit side-chains REVERT: B 14 GLU cc_start: 0.8540 (tp30) cc_final: 0.8251 (tp30) REVERT: B 254 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8493 (tp) REVERT: G 44 HIS cc_start: 0.8166 (m170) cc_final: 0.7911 (m170) REVERT: G 48 ASP cc_start: 0.8121 (t0) cc_final: 0.7492 (t0) REVERT: H 106 SER cc_start: 0.9200 (t) cc_final: 0.8717 (p) REVERT: H 231 GLN cc_start: 0.8553 (pp30) cc_final: 0.8126 (pp30) REVERT: R 216 ARG cc_start: 0.7195 (mtt180) cc_final: 0.6930 (mtt-85) outliers start: 25 outliers final: 21 residues processed: 132 average time/residue: 0.1873 time to fit residues: 34.4219 Evaluate side-chains 133 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 255 PHE Chi-restraints excluded: chain R residue 269 TYR Chi-restraints excluded: chain R residue 272 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.0070 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 HIS H 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8018 Z= 0.196 Angle : 0.495 6.321 10954 Z= 0.265 Chirality : 0.041 0.164 1281 Planarity : 0.004 0.039 1415 Dihedral : 6.346 144.776 1186 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.06 % Allowed : 15.67 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.73 (0.26), residues: 1100 helix: 2.12 (0.28), residues: 361 sheet: -0.31 (0.31), residues: 247 loop : -0.26 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS C 91 PHE 0.013 0.001 PHE C 199 TYR 0.019 0.001 TYR B 297 ARG 0.007 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 0.854 Fit side-chains REVERT: B 14 GLU cc_start: 0.8542 (tp30) cc_final: 0.8283 (tp30) REVERT: B 254 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8452 (tp) REVERT: G 44 HIS cc_start: 0.8190 (m170) cc_final: 0.7967 (m170) REVERT: G 48 ASP cc_start: 0.8149 (t0) cc_final: 0.7470 (t0) REVERT: H 106 SER cc_start: 0.9208 (t) cc_final: 0.8711 (p) REVERT: H 231 GLN cc_start: 0.8541 (pp30) cc_final: 0.8121 (pp30) REVERT: R 216 ARG cc_start: 0.7173 (mtt180) cc_final: 0.6908 (mtt-85) outliers start: 28 outliers final: 22 residues processed: 137 average time/residue: 0.1825 time to fit residues: 34.6911 Evaluate side-chains 137 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 269 TYR Chi-restraints excluded: chain R residue 272 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 93 optimal weight: 0.0060 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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: 0.7699 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8018 Z= 0.197 Angle : 0.509 10.074 10954 Z= 0.270 Chirality : 0.041 0.165 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.082 145.104 1184 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.34 % Allowed : 17.56 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.74 (0.26), residues: 1100 helix: 2.18 (0.28), residues: 360 sheet: -0.35 (0.31), residues: 247 loop : -0.25 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS C 91 PHE 0.013 0.001 PHE C 199 TYR 0.020 0.001 TYR B 297 ARG 0.007 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.907 Fit side-chains REVERT: B 14 GLU cc_start: 0.8544 (tp30) cc_final: 0.8288 (tp30) REVERT: B 254 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8430 (tp) REVERT: B 331 ASN cc_start: 0.8060 (m-40) cc_final: 0.7803 (p0) REVERT: G 44 HIS cc_start: 0.8182 (m170) cc_final: 0.7964 (m170) REVERT: G 48 ASP cc_start: 0.8178 (t0) cc_final: 0.7489 (t0) REVERT: H 106 SER cc_start: 0.9203 (t) cc_final: 0.8911 (t) REVERT: H 183 GLN cc_start: 0.7745 (mt0) cc_final: 0.7481 (tt0) REVERT: H 231 GLN cc_start: 0.8516 (pp30) cc_final: 0.8098 (pp30) REVERT: R 216 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6911 (mtt-85) outliers start: 23 outliers final: 21 residues processed: 129 average time/residue: 0.1839 time to fit residues: 32.8471 Evaluate side-chains 132 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 269 TYR Chi-restraints excluded: chain R residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 53 optimal weight: 0.0970 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8018 Z= 0.168 Angle : 0.497 9.814 10954 Z= 0.263 Chirality : 0.041 0.166 1281 Planarity : 0.004 0.038 1415 Dihedral : 6.005 145.626 1184 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.76 % Allowed : 17.85 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.76 (0.26), residues: 1100 helix: 2.17 (0.28), residues: 360 sheet: -0.29 (0.31), residues: 245 loop : -0.25 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE C 199 TYR 0.019 0.001 TYR B 297 ARG 0.007 0.000 ARG R 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.914 Fit side-chains REVERT: B 14 GLU cc_start: 0.8527 (tp30) cc_final: 0.8236 (tp30) REVERT: B 254 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8360 (tp) REVERT: B 290 GLU cc_start: 0.8394 (pm20) cc_final: 0.8033 (pm20) REVERT: G 44 HIS cc_start: 0.8148 (m170) cc_final: 0.7929 (m170) REVERT: G 48 ASP cc_start: 0.8170 (t0) cc_final: 0.7477 (t0) REVERT: H 106 SER cc_start: 0.9160 (t) cc_final: 0.8869 (t) REVERT: H 183 GLN cc_start: 0.7746 (mt0) cc_final: 0.7475 (tt0) REVERT: H 231 GLN cc_start: 0.8497 (pp30) cc_final: 0.8086 (pp30) REVERT: R 216 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6705 (mmm-85) outliers start: 19 outliers final: 16 residues processed: 124 average time/residue: 0.1854 time to fit residues: 31.9562 Evaluate side-chains 128 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 269 TYR Chi-restraints excluded: chain R residue 272 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.171995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114197 restraints weight = 9592.759| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.87 r_work: 0.3246 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8018 Z= 0.214 Angle : 0.516 9.884 10954 Z= 0.274 Chirality : 0.042 0.165 1281 Planarity : 0.004 0.039 1415 Dihedral : 6.065 145.387 1184 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.05 % Allowed : 17.85 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1100 helix: 2.18 (0.29), residues: 360 sheet: -0.43 (0.31), residues: 250 loop : -0.25 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.004 0.001 HIS C 91 PHE 0.014 0.001 PHE C 199 TYR 0.019 0.001 TYR B 297 ARG 0.007 0.000 ARG R 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1983.93 seconds wall clock time: 36 minutes 42.58 seconds (2202.58 seconds total)