Starting phenix.real_space_refine on Fri Jul 19 17:41:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/07_2024/8uwl_42676.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/07_2024/8uwl_42676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/07_2024/8uwl_42676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/07_2024/8uwl_42676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/07_2024/8uwl_42676.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uwl_42676/07_2024/8uwl_42676.cif" } resolution = 2.8 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= 0.001 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5495 2.51 5 N 1470 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8626 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2084 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1792 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2592 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 396 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1737 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H8G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.47, per 1000 atoms: 0.63 Number of scatterers: 8626 At special positions: 0 Unit cell: (115.886, 100.548, 134.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1604 8.00 N 1470 7.00 C 5495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.34 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=1.90 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: 3.24 Conformation dependent library (CDL) restraints added in 1.8 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 39.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 78 through 101 removed outlier: 3.574A pdb=" N ALA A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 126 removed outlier: 3.530A pdb=" N TYR A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.826A pdb=" N VAL A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 132 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 179 removed outlier: 3.712A pdb=" N TRP A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.579A pdb=" N HIS A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 208 removed outlier: 3.671A pdb=" N SER A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 233 through 243 removed outlier: 3.533A pdb=" N PHE A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 266 Processing helix chain 'A' and resid 313 through 349 Proline residue: A 338 - end of helix removed outlier: 3.657A pdb=" N THR A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 383 removed outlier: 3.809A pdb=" N GLY A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Proline residue: A 377 - end of helix removed outlier: 3.613A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N PHE A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 397 removed outlier: 3.719A pdb=" N ARG A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.512A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.791A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.230A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 removed outlier: 3.890A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.750A pdb=" N GLU B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.519A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 10 through 24 removed outlier: 3.565A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.631A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.535A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.423A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 76 removed outlier: 4.144A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.708A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.703A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.954A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.956A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.879A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.644A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.799A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.517A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.517A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.770A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.770A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1230 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: 2.74 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1619 1.32 - 1.45: 2212 1.45 - 1.57: 4890 1.57 - 1.69: 0 1.69 - 1.82: 85 Bond restraints: 8806 Sorted by residual: bond pdb=" N VAL E 135 " pdb=" CA VAL E 135 " ideal model delta sigma weight residual 1.454 1.497 -0.043 7.70e-03 1.69e+04 3.08e+01 bond pdb=" N ILE C 93 " pdb=" CA ILE C 93 " ideal model delta sigma weight residual 1.456 1.497 -0.041 8.70e-03 1.32e+04 2.19e+01 bond pdb=" N VAL E 48 " pdb=" CA VAL E 48 " ideal model delta sigma weight residual 1.458 1.495 -0.037 9.00e-03 1.23e+04 1.71e+01 bond pdb=" N VAL B 5 " pdb=" CA VAL B 5 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.19e-02 7.06e+03 1.70e+01 bond pdb=" N MET A 128 " pdb=" CA MET A 128 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.04e-02 9.25e+03 1.61e+01 ... (remaining 8801 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.67: 273 106.67 - 113.89: 4737 113.89 - 121.11: 4392 121.11 - 128.32: 2493 128.32 - 135.54: 63 Bond angle restraints: 11958 Sorted by residual: angle pdb=" N ASN B 43 " pdb=" CA ASN B 43 " pdb=" C ASN B 43 " ideal model delta sigma weight residual 113.17 104.43 8.74 1.26e+00 6.30e-01 4.81e+01 angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 112.59 104.16 8.43 1.22e+00 6.72e-01 4.78e+01 angle pdb=" CA GLY E 114 " pdb=" C GLY E 114 " pdb=" O GLY E 114 " ideal model delta sigma weight residual 122.22 117.75 4.47 6.50e-01 2.37e+00 4.73e+01 angle pdb=" N THR A 190 " pdb=" CA THR A 190 " pdb=" C THR A 190 " ideal model delta sigma weight residual 113.41 105.26 8.15 1.22e+00 6.72e-01 4.46e+01 angle pdb=" C PRO B 184 " pdb=" CA PRO B 184 " pdb=" CB PRO B 184 " ideal model delta sigma weight residual 112.62 102.02 10.60 1.65e+00 3.67e-01 4.13e+01 ... (remaining 11953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 5149 35.54 - 71.07: 74 71.07 - 106.60: 1 106.60 - 142.14: 0 142.14 - 177.67: 2 Dihedral angle restraints: 5226 sinusoidal: 1970 harmonic: 3256 Sorted by residual: dihedral pdb=" C THR E 198 " pdb=" N THR E 198 " pdb=" CA THR E 198 " pdb=" CB THR E 198 " ideal model delta harmonic sigma weight residual -122.00 -137.73 15.73 0 2.50e+00 1.60e-01 3.96e+01 dihedral pdb=" N THR E 198 " pdb=" C THR E 198 " pdb=" CA THR E 198 " pdb=" CB THR E 198 " ideal model delta harmonic sigma weight residual 123.40 137.37 -13.97 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C PRO B 184 " pdb=" N PRO B 184 " pdb=" CA PRO B 184 " pdb=" CB PRO B 184 " ideal model delta harmonic sigma weight residual -120.70 -107.32 -13.38 0 2.50e+00 1.60e-01 2.87e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 839 0.113 - 0.226: 459 0.226 - 0.339: 71 0.339 - 0.452: 2 0.452 - 0.565: 1 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CA THR E 198 " pdb=" N THR E 198 " pdb=" C THR E 198 " pdb=" CB THR E 198 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.56 2.00e-01 2.50e+01 7.98e+00 chirality pdb=" CA HIS B 209 " pdb=" N HIS B 209 " pdb=" C HIS B 209 " pdb=" CB HIS B 209 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ASP C 153 " pdb=" N ASP C 153 " pdb=" C ASP C 153 " pdb=" CB ASP C 153 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 1369 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAF H8G A 501 " -0.113 2.00e-02 2.50e+03 8.88e-02 2.17e+02 pdb=" CAG H8G A 501 " -0.078 2.00e-02 2.50e+03 pdb=" CAH H8G A 501 " -0.012 2.00e-02 2.50e+03 pdb=" CAI H8G A 501 " -0.015 2.00e-02 2.50e+03 pdb=" CAL H8G A 501 " -0.179 2.00e-02 2.50e+03 pdb=" CAQ H8G A 501 " 0.116 2.00e-02 2.50e+03 pdb=" CAR H8G A 501 " 0.007 2.00e-02 2.50e+03 pdb=" CAS H8G A 501 " 0.067 2.00e-02 2.50e+03 pdb=" CAT H8G A 501 " 0.081 2.00e-02 2.50e+03 pdb=" CAU H8G A 501 " 0.101 2.00e-02 2.50e+03 pdb=" NAO H8G A 501 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAJ H8G A 501 " 0.058 2.00e-02 2.50e+03 1.04e-01 1.89e+02 pdb=" CAK H8G A 501 " 0.024 2.00e-02 2.50e+03 pdb=" CAP H8G A 501 " -0.065 2.00e-02 2.50e+03 pdb=" CAV H8G A 501 " 0.160 2.00e-02 2.50e+03 pdb=" NAN H8G A 501 " -0.203 2.00e-02 2.50e+03 pdb=" NAY H8G A 501 " 0.017 2.00e-02 2.50e+03 pdb=" OAD H8G A 501 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAE H8G A 501 " -0.036 2.00e-02 2.50e+03 2.26e-02 6.37e+00 pdb=" CAQ H8G A 501 " -0.008 2.00e-02 2.50e+03 pdb=" CAS H8G A 501 " 0.021 2.00e-02 2.50e+03 pdb=" CAV H8G A 501 " 0.027 2.00e-02 2.50e+03 pdb=" CAW H8G A 501 " -0.005 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 72 2.64 - 3.21: 7191 3.21 - 3.77: 11699 3.77 - 4.34: 16596 4.34 - 4.90: 28096 Nonbonded interactions: 63654 Sorted by model distance: nonbonded pdb=" O SER A 131 " pdb=" OG1 THR A 134 " model vdw 2.079 2.440 nonbonded pdb=" O ASN A 233 " pdb=" ND2 ASN A 233 " model vdw 2.286 2.520 nonbonded pdb=" O ALA A 78 " pdb=" OG1 THR A 81 " model vdw 2.310 2.440 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.310 2.440 nonbonded pdb=" OD1 ASP B 147 " pdb=" N LEU B 148 " model vdw 2.325 2.520 ... (remaining 63649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.013 0.056 8806 Z= 0.851 Angle : 1.689 10.601 11958 Z= 1.290 Chirality : 0.121 0.565 1372 Planarity : 0.006 0.104 1517 Dihedral : 12.383 177.669 3113 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.43 % Allowed : 3.07 % Favored : 95.50 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.23), residues: 1105 helix: 2.54 (0.25), residues: 377 sheet: 2.30 (0.37), residues: 173 loop : -0.11 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 82 HIS 0.008 0.003 HIS E 35 PHE 0.033 0.003 PHE C 151 TYR 0.020 0.003 TYR E 102 ARG 0.005 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 226 time to evaluate : 0.903 Fit side-chains REVERT: A 219 SER cc_start: 0.6894 (p) cc_final: 0.6665 (m) REVERT: A 222 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6477 (t80) REVERT: A 227 CYS cc_start: 0.6529 (t) cc_final: 0.6278 (t) REVERT: A 345 MET cc_start: 0.7399 (ttm) cc_final: 0.7193 (ttt) REVERT: C 37 ILE cc_start: 0.7653 (mm) cc_final: 0.7348 (pt) REVERT: C 246 ASP cc_start: 0.7566 (p0) cc_final: 0.7327 (p0) REVERT: C 325 MET cc_start: 0.8526 (mmt) cc_final: 0.7856 (mmt) REVERT: E 34 MET cc_start: 0.9209 (mmm) cc_final: 0.8933 (mmt) REVERT: E 211 ASP cc_start: 0.7828 (m-30) cc_final: 0.7548 (m-30) outliers start: 13 outliers final: 3 residues processed: 234 average time/residue: 1.1566 time to fit residues: 287.7860 Evaluate side-chains 159 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 113 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN B 146 GLN E 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8806 Z= 0.232 Angle : 0.631 7.175 11958 Z= 0.358 Chirality : 0.046 0.175 1372 Planarity : 0.005 0.040 1517 Dihedral : 9.513 172.690 1245 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.40 % Allowed : 12.40 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.24), residues: 1105 helix: 2.97 (0.26), residues: 388 sheet: 1.61 (0.29), residues: 281 loop : -0.26 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.004 0.001 HIS C 91 PHE 0.024 0.002 PHE C 151 TYR 0.017 0.002 TYR A 370 ARG 0.007 0.001 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 0.844 Fit side-chains REVERT: A 222 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6774 (t80) REVERT: A 345 MET cc_start: 0.7242 (ttm) cc_final: 0.7022 (ttt) REVERT: A 363 ASN cc_start: 0.7187 (m110) cc_final: 0.6894 (m110) REVERT: C 32 GLN cc_start: 0.8484 (mt0) cc_final: 0.8188 (mt0) REVERT: C 175 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: C 234 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8238 (t80) REVERT: C 325 MET cc_start: 0.8363 (mmt) cc_final: 0.8084 (mmt) REVERT: E 85 SER cc_start: 0.8381 (m) cc_final: 0.8178 (t) REVERT: E 211 ASP cc_start: 0.7657 (m-30) cc_final: 0.7456 (m-30) outliers start: 31 outliers final: 7 residues processed: 175 average time/residue: 1.1655 time to fit residues: 217.2461 Evaluate side-chains 145 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 71 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN C 237 ASN D 18 GLN E 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8806 Z= 0.223 Angle : 0.585 7.315 11958 Z= 0.329 Chirality : 0.044 0.156 1372 Planarity : 0.004 0.040 1517 Dihedral : 9.127 170.581 1242 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.95 % Allowed : 15.37 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1105 helix: 3.07 (0.26), residues: 388 sheet: 1.43 (0.29), residues: 286 loop : -0.54 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.022 0.002 PHE C 151 TYR 0.014 0.001 TYR A 370 ARG 0.009 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 345 MET cc_start: 0.7262 (ttm) cc_final: 0.7023 (ttt) REVERT: C 32 GLN cc_start: 0.8488 (mt0) cc_final: 0.8171 (mt0) REVERT: C 175 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: C 258 ASP cc_start: 0.7087 (t0) cc_final: 0.6596 (t0) REVERT: C 325 MET cc_start: 0.8445 (mmt) cc_final: 0.8089 (mmt) REVERT: E 211 ASP cc_start: 0.7663 (m-30) cc_final: 0.7446 (m-30) outliers start: 36 outliers final: 17 residues processed: 169 average time/residue: 1.1888 time to fit residues: 213.9719 Evaluate side-chains 157 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 44 GLN C 237 ASN E 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8806 Z= 0.184 Angle : 0.540 6.801 11958 Z= 0.302 Chirality : 0.042 0.147 1372 Planarity : 0.004 0.039 1517 Dihedral : 8.905 171.618 1240 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.17 % Allowed : 16.58 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.25), residues: 1105 helix: 3.13 (0.26), residues: 388 sheet: 1.31 (0.29), residues: 287 loop : -0.67 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 141 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.001 PHE C 151 TYR 0.011 0.001 TYR E 95 ARG 0.007 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 345 MET cc_start: 0.7276 (ttm) cc_final: 0.7032 (ttt) REVERT: B 185 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6483 (mtm-85) REVERT: C 32 GLN cc_start: 0.8479 (mt0) cc_final: 0.8150 (mt0) REVERT: C 175 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: C 234 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8273 (t80) REVERT: C 256 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7558 (mtp180) REVERT: C 258 ASP cc_start: 0.7066 (t0) cc_final: 0.6630 (t0) REVERT: C 325 MET cc_start: 0.8453 (mmt) cc_final: 0.8095 (mmt) REVERT: E 211 ASP cc_start: 0.7655 (m-30) cc_final: 0.7403 (m-30) outliers start: 38 outliers final: 19 residues processed: 163 average time/residue: 1.1254 time to fit residues: 195.7957 Evaluate side-chains 158 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.0010 chunk 0 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN C 44 GLN C 237 ASN E 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8806 Z= 0.177 Angle : 0.522 6.384 11958 Z= 0.291 Chirality : 0.042 0.142 1372 Planarity : 0.004 0.039 1517 Dihedral : 8.828 171.243 1240 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.61 % Allowed : 17.01 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.25), residues: 1105 helix: 3.18 (0.26), residues: 387 sheet: 1.17 (0.30), residues: 287 loop : -0.68 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 141 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE C 151 TYR 0.011 0.001 TYR E 178 ARG 0.005 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 345 MET cc_start: 0.7329 (ttm) cc_final: 0.7091 (ttt) REVERT: B 6 SER cc_start: 0.6491 (OUTLIER) cc_final: 0.6276 (p) REVERT: B 9 ASP cc_start: 0.6788 (m-30) cc_final: 0.6517 (m-30) REVERT: B 185 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6452 (mtm-85) REVERT: C 32 GLN cc_start: 0.8479 (mt0) cc_final: 0.8157 (mt0) REVERT: C 175 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8116 (mp10) REVERT: C 234 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8268 (t80) REVERT: C 256 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7570 (mtp180) REVERT: C 258 ASP cc_start: 0.7131 (t0) cc_final: 0.6722 (t0) REVERT: C 325 MET cc_start: 0.8450 (mmt) cc_final: 0.8089 (mmt) REVERT: E 211 ASP cc_start: 0.7642 (m-30) cc_final: 0.7394 (m-30) outliers start: 42 outliers final: 21 residues processed: 158 average time/residue: 1.0931 time to fit residues: 184.2543 Evaluate side-chains 162 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.0050 chunk 55 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8806 Z= 0.169 Angle : 0.510 6.242 11958 Z= 0.284 Chirality : 0.041 0.141 1372 Planarity : 0.004 0.037 1517 Dihedral : 8.774 171.077 1240 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.62 % Allowed : 18.77 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.25), residues: 1105 helix: 3.14 (0.26), residues: 390 sheet: 1.10 (0.30), residues: 287 loop : -0.75 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 141 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE C 151 TYR 0.011 0.001 TYR E 178 ARG 0.006 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 262 GLN cc_start: 0.7582 (mm110) cc_final: 0.7378 (mt0) REVERT: A 345 MET cc_start: 0.7325 (ttm) cc_final: 0.7100 (ttt) REVERT: B 9 ASP cc_start: 0.6820 (m-30) cc_final: 0.6563 (m-30) REVERT: B 185 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6443 (mtm-85) REVERT: C 32 GLN cc_start: 0.8481 (mt0) cc_final: 0.8236 (mt0) REVERT: C 43 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.8014 (mp) REVERT: C 175 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: C 234 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8264 (t80) REVERT: C 256 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7519 (mtp180) REVERT: C 258 ASP cc_start: 0.7115 (t0) cc_final: 0.6768 (t0) REVERT: C 325 MET cc_start: 0.8450 (mmt) cc_final: 0.8087 (mmt) REVERT: E 211 ASP cc_start: 0.7604 (m-30) cc_final: 0.7333 (m-30) outliers start: 33 outliers final: 18 residues processed: 155 average time/residue: 1.1975 time to fit residues: 197.3774 Evaluate side-chains 155 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN E 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8806 Z= 0.203 Angle : 0.535 7.014 11958 Z= 0.297 Chirality : 0.042 0.144 1372 Planarity : 0.004 0.046 1517 Dihedral : 8.676 170.597 1238 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.73 % Allowed : 18.88 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1105 helix: 3.03 (0.26), residues: 390 sheet: 1.03 (0.30), residues: 287 loop : -0.82 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.001 PHE C 151 TYR 0.011 0.001 TYR E 95 ARG 0.011 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 345 MET cc_start: 0.7339 (ttm) cc_final: 0.7111 (ttt) REVERT: B 185 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6487 (mtm-85) REVERT: C 32 GLN cc_start: 0.8481 (mt0) cc_final: 0.8252 (mt0) REVERT: C 43 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8022 (mp) REVERT: C 234 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8260 (t80) REVERT: C 256 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7522 (mtp180) REVERT: C 258 ASP cc_start: 0.7157 (t0) cc_final: 0.6747 (t0) REVERT: C 325 MET cc_start: 0.8446 (mmt) cc_final: 0.8024 (mmt) REVERT: E 211 ASP cc_start: 0.7611 (m-30) cc_final: 0.7350 (m-30) outliers start: 34 outliers final: 21 residues processed: 153 average time/residue: 1.2338 time to fit residues: 200.8395 Evaluate side-chains 154 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 9 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8806 Z= 0.171 Angle : 0.511 6.537 11958 Z= 0.283 Chirality : 0.041 0.138 1372 Planarity : 0.004 0.038 1517 Dihedral : 8.631 170.543 1238 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.62 % Allowed : 19.43 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1105 helix: 3.07 (0.26), residues: 391 sheet: 0.97 (0.29), residues: 288 loop : -0.81 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE C 151 TYR 0.011 0.001 TYR E 178 ARG 0.009 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 208 MET cc_start: 0.8124 (tpp) cc_final: 0.7923 (tpt) REVERT: A 345 MET cc_start: 0.7331 (ttm) cc_final: 0.7102 (ttt) REVERT: B 185 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6411 (mtm-85) REVERT: C 32 GLN cc_start: 0.8487 (mt0) cc_final: 0.8252 (mt0) REVERT: C 43 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8004 (mp) REVERT: C 215 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: C 234 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8260 (t80) REVERT: C 256 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7513 (mtp180) REVERT: C 258 ASP cc_start: 0.7140 (t0) cc_final: 0.6786 (t0) REVERT: C 325 MET cc_start: 0.8455 (mmt) cc_final: 0.8028 (mmt) REVERT: E 211 ASP cc_start: 0.7595 (m-30) cc_final: 0.7336 (m-30) outliers start: 33 outliers final: 20 residues processed: 149 average time/residue: 1.1488 time to fit residues: 182.6519 Evaluate side-chains 151 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN E 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8806 Z= 0.215 Angle : 0.543 7.587 11958 Z= 0.300 Chirality : 0.042 0.140 1372 Planarity : 0.004 0.038 1517 Dihedral : 8.660 170.054 1238 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.18 % Allowed : 19.65 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1105 helix: 3.01 (0.26), residues: 388 sheet: 0.91 (0.29), residues: 288 loop : -0.84 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE C 151 TYR 0.011 0.001 TYR E 95 ARG 0.009 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 345 MET cc_start: 0.7346 (ttm) cc_final: 0.7115 (ttt) REVERT: B 185 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6489 (mtm-85) REVERT: C 32 GLN cc_start: 0.8487 (mt0) cc_final: 0.8252 (mt0) REVERT: C 43 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8008 (mp) REVERT: C 79 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9016 (mp) REVERT: C 234 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8253 (t80) REVERT: C 256 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7542 (mtp180) REVERT: C 258 ASP cc_start: 0.7113 (t0) cc_final: 0.6702 (t0) REVERT: C 325 MET cc_start: 0.8466 (mmt) cc_final: 0.7990 (mmt) REVERT: E 211 ASP cc_start: 0.7634 (m-30) cc_final: 0.7344 (m-30) outliers start: 29 outliers final: 22 residues processed: 151 average time/residue: 1.1518 time to fit residues: 185.3790 Evaluate side-chains 155 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 86 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN E 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8806 Z= 0.193 Angle : 0.530 7.322 11958 Z= 0.293 Chirality : 0.042 0.138 1372 Planarity : 0.004 0.059 1517 Dihedral : 8.636 169.960 1238 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.96 % Allowed : 19.87 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1105 helix: 3.03 (0.26), residues: 388 sheet: 0.89 (0.30), residues: 288 loop : -0.85 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.011 0.001 TYR E 95 ARG 0.015 0.001 ARG C 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 345 MET cc_start: 0.7341 (ttm) cc_final: 0.7107 (ttt) REVERT: B 185 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6474 (mtm-85) REVERT: B 243 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6927 (t80) REVERT: C 32 GLN cc_start: 0.8487 (mt0) cc_final: 0.8250 (mt0) REVERT: C 43 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7990 (mp) REVERT: C 79 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8993 (mp) REVERT: C 234 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8253 (t80) REVERT: C 256 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7539 (mtp180) REVERT: C 258 ASP cc_start: 0.7116 (t0) cc_final: 0.6721 (t0) REVERT: C 325 MET cc_start: 0.8463 (mmt) cc_final: 0.7931 (mmt) REVERT: E 211 ASP cc_start: 0.7639 (m-30) cc_final: 0.7364 (m-30) outliers start: 27 outliers final: 19 residues processed: 145 average time/residue: 1.1720 time to fit residues: 180.9151 Evaluate side-chains 151 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 243 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 86 optimal weight: 0.0020 chunk 36 optimal weight: 0.0050 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.104437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.090611 restraints weight = 14404.163| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.01 r_work: 0.3184 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8806 Z= 0.160 Angle : 0.504 6.798 11958 Z= 0.279 Chirality : 0.041 0.132 1372 Planarity : 0.004 0.060 1517 Dihedral : 8.585 170.278 1238 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.52 % Allowed : 20.53 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1105 helix: 3.05 (0.26), residues: 391 sheet: 0.85 (0.29), residues: 296 loop : -0.87 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE C 199 TYR 0.010 0.001 TYR E 178 ARG 0.014 0.000 ARG C 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3807.22 seconds wall clock time: 66 minutes 53.69 seconds (4013.69 seconds total)