Starting phenix.real_space_refine on Tue Jun 25 20:30:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/06_2024/8ykx_39375_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/06_2024/8ykx_39375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/06_2024/8ykx_39375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/06_2024/8ykx_39375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/06_2024/8ykx_39375_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykx_39375/06_2024/8ykx_39375_neut_updated.pdb" } resolution = 2.69 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= 0.079 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 56 5.16 5 C 5576 2.51 5 N 1472 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 33": "OE1" <-> "OE2" Residue "R GLU 153": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8710 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2276 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 268} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1699 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 210} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2558 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1728 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 441 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'MAE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.91, per 1000 atoms: 0.56 Number of scatterers: 8710 At special positions: 0 Unit cell: (86.87, 119.72, 132.13, 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 56 16.00 O 1606 8.00 N 1472 7.00 C 5576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.61 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: 3.34 Conformation dependent library (CDL) restraints added in 1.7 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 35.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'R' and resid 12 through 48 removed outlier: 4.065A pdb=" N ALA R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA R 20 " --> pdb=" O ALA R 16 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU R 26 " --> pdb=" O GLU R 22 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER R 27 " --> pdb=" O LYS R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 85 removed outlier: 3.768A pdb=" N THR R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU R 76 " --> pdb=" O PHE R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 92 through 125 Processing helix chain 'R' and resid 132 through 134 No H-bonds generated for 'chain 'R' and resid 132 through 134' Processing helix chain 'R' and resid 136 through 157 Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 181 through 195 Processing helix chain 'R' and resid 197 through 216 Processing helix chain 'R' and resid 228 through 259 removed outlier: 3.577A pdb=" N VAL R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) Proline residue: R 247 - end of helix removed outlier: 3.564A pdb=" N ARG R 259 " --> pdb=" O ARG R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 296 Proline residue: R 282 - end of helix removed outlier: 4.069A pdb=" N ASN R 287 " --> pdb=" O LEU R 283 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL R 289 " --> pdb=" O PHE R 285 " (cutoff:3.500A) Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 300 through 308 Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 52 removed outlier: 4.271A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.151A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.582A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.790A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.720A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.876A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.785A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.783A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.682A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.807A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.491A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.391A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.472A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.019A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.509A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.163A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1173 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: 2.46 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2190 1.33 - 1.45: 1820 1.45 - 1.58: 4796 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 8888 Sorted by residual: bond pdb=" C LEU R 214 " pdb=" N LYS R 215 " ideal model delta sigma weight residual 1.335 1.431 -0.097 1.36e-02 5.41e+03 5.05e+01 bond pdb=" C PHE R 296 " pdb=" N LEU R 297 " ideal model delta sigma weight residual 1.334 1.410 -0.076 1.43e-02 4.89e+03 2.83e+01 bond pdb=" CA ARG R 281 " pdb=" C ARG R 281 " ideal model delta sigma weight residual 1.521 1.571 -0.049 1.17e-02 7.31e+03 1.78e+01 bond pdb=" C ARG R 281 " pdb=" N PRO R 282 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.28e-02 6.10e+03 1.36e+01 bond pdb=" N THR R 269 " pdb=" CA THR R 269 " ideal model delta sigma weight residual 1.458 1.411 0.047 1.90e-02 2.77e+03 6.15e+00 ... (remaining 8883 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.88: 206 106.88 - 113.67: 4945 113.67 - 120.46: 3370 120.46 - 127.25: 3435 127.25 - 134.04: 91 Bond angle restraints: 12047 Sorted by residual: angle pdb=" N LEU R 231 " pdb=" CA LEU R 231 " pdb=" C LEU R 231 " ideal model delta sigma weight residual 111.28 105.84 5.44 1.09e+00 8.42e-01 2.50e+01 angle pdb=" N THR R 269 " pdb=" CA THR R 269 " pdb=" C THR R 269 " ideal model delta sigma weight residual 111.00 100.08 10.92 2.80e+00 1.28e-01 1.52e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 128.04 -6.50 1.91e+00 2.74e-01 1.16e+01 angle pdb=" N VAL A 201 " pdb=" CA VAL A 201 " pdb=" C VAL A 201 " ideal model delta sigma weight residual 111.91 109.26 2.65 8.90e-01 1.26e+00 8.89e+00 angle pdb=" N ASP A 251 " pdb=" CA ASP A 251 " pdb=" C ASP A 251 " ideal model delta sigma weight residual 111.07 108.12 2.95 1.07e+00 8.73e-01 7.59e+00 ... (remaining 12042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4721 17.53 - 35.07: 400 35.07 - 52.60: 110 52.60 - 70.13: 17 70.13 - 87.66: 12 Dihedral angle restraints: 5260 sinusoidal: 2003 harmonic: 3257 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 50.10 42.90 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ILE R 89 " pdb=" C ILE R 89 " pdb=" N TYR R 90 " pdb=" CA TYR R 90 " ideal model delta harmonic sigma weight residual -180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 951 0.035 - 0.070: 286 0.070 - 0.105: 101 0.105 - 0.140: 40 0.140 - 0.175: 4 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA LYS R 135 " pdb=" N LYS R 135 " pdb=" C LYS R 135 " pdb=" CB LYS R 135 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA THR R 269 " pdb=" N THR R 269 " pdb=" C THR R 269 " pdb=" CB THR R 269 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CB THR R 280 " pdb=" CA THR R 280 " pdb=" OG1 THR R 280 " pdb=" CG2 THR R 280 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1379 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 296 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.51e+00 pdb=" C PHE R 296 " 0.047 2.00e-02 2.50e+03 pdb=" O PHE R 296 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU R 297 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 134 " 0.166 9.50e-02 1.11e+02 7.47e-02 3.75e+00 pdb=" NE ARG B 134 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 134 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 134 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 134 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 280 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C THR R 280 " 0.031 2.00e-02 2.50e+03 pdb=" O THR R 280 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG R 281 " -0.011 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1411 2.76 - 3.29: 8561 3.29 - 3.83: 14784 3.83 - 4.36: 18353 4.36 - 4.90: 31856 Nonbonded interactions: 74965 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.222 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.305 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.312 2.440 nonbonded pdb=" O SER R 82 " pdb=" N GLY R 86 " model vdw 2.344 2.520 ... (remaining 74960 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: 0.810 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: 3.800 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.010 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.004 0.097 8888 Z= 0.272 Angle : 0.609 10.915 12047 Z= 0.337 Chirality : 0.042 0.175 1382 Planarity : 0.004 0.075 1518 Dihedral : 14.755 87.663 3155 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.43 % Allowed : 13.73 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1097 helix: 2.06 (0.27), residues: 388 sheet: 0.55 (0.31), residues: 277 loop : -0.01 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.003 0.001 HIS R 103 PHE 0.009 0.001 PHE R 205 TYR 0.013 0.001 TYR E 103 ARG 0.010 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 203 MET cc_start: 0.8417 (ttm) cc_final: 0.8195 (mtp) REVERT: R 281 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7163 (ttm170) REVERT: A 29 LYS cc_start: 0.7862 (tttt) cc_final: 0.7484 (tmmt) REVERT: A 242 ARG cc_start: 0.7933 (mtt180) cc_final: 0.7579 (mtm180) REVERT: A 333 GLN cc_start: 0.7529 (tp40) cc_final: 0.7121 (tp-100) REVERT: B 212 ASP cc_start: 0.7579 (t70) cc_final: 0.7157 (t70) REVERT: B 259 GLN cc_start: 0.8066 (pt0) cc_final: 0.7608 (pt0) outliers start: 4 outliers final: 1 residues processed: 154 average time/residue: 1.4338 time to fit residues: 232.5728 Evaluate side-chains 141 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 281 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 220 GLN R 301 HIS A 188 HIS A 269 ASN A 306 GLN A 331 ASN E 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8888 Z= 0.204 Angle : 0.532 6.288 12047 Z= 0.282 Chirality : 0.042 0.145 1382 Planarity : 0.004 0.056 1518 Dihedral : 5.160 84.727 1214 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.04 % Allowed : 13.20 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1097 helix: 2.26 (0.26), residues: 387 sheet: 0.46 (0.30), residues: 271 loop : 0.13 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS R 301 PHE 0.011 0.001 PHE R 72 TYR 0.012 0.001 TYR E 103 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: R 203 MET cc_start: 0.8515 (ttm) cc_final: 0.8309 (mtp) REVERT: R 288 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 29 LYS cc_start: 0.7869 (tttt) cc_final: 0.7453 (tmmt) REVERT: A 306 GLN cc_start: 0.7549 (mt0) cc_final: 0.7321 (tt0) REVERT: A 333 GLN cc_start: 0.7597 (tp40) cc_final: 0.7136 (tp-100) REVERT: B 212 ASP cc_start: 0.7450 (t70) cc_final: 0.7055 (OUTLIER) REVERT: B 259 GLN cc_start: 0.8037 (pt0) cc_final: 0.7599 (pt0) REVERT: E 157 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8278 (mp) REVERT: E 160 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6622 (mtm110) REVERT: E 163 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7656 (ttpt) outliers start: 19 outliers final: 3 residues processed: 151 average time/residue: 1.3550 time to fit residues: 216.4407 Evaluate side-chains 137 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain E residue 157 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 0.0270 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 52 GLN A 188 HIS A 269 ASN A 331 ASN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8888 Z= 0.133 Angle : 0.488 7.990 12047 Z= 0.256 Chirality : 0.041 0.130 1382 Planarity : 0.003 0.041 1518 Dihedral : 4.695 84.067 1209 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.04 % Allowed : 14.70 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1097 helix: 2.28 (0.26), residues: 395 sheet: 0.54 (0.30), residues: 269 loop : 0.16 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE B 199 TYR 0.010 0.001 TYR R 107 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 79 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8109 (mm) REVERT: A 29 LYS cc_start: 0.7817 (tttt) cc_final: 0.7418 (tmmt) REVERT: A 251 ASP cc_start: 0.8589 (t70) cc_final: 0.8199 (t0) REVERT: A 333 GLN cc_start: 0.7612 (tp40) cc_final: 0.6980 (tp-100) REVERT: A 337 ASP cc_start: 0.7892 (m-30) cc_final: 0.7557 (m-30) REVERT: B 212 ASP cc_start: 0.7304 (t70) cc_final: 0.6940 (t0) REVERT: B 259 GLN cc_start: 0.8036 (pt0) cc_final: 0.7569 (pt0) REVERT: B 262 MET cc_start: 0.8562 (ttm) cc_final: 0.8352 (ttm) REVERT: E 157 ILE cc_start: 0.8550 (mm) cc_final: 0.8201 (mp) REVERT: E 213 THR cc_start: 0.8038 (t) cc_final: 0.7796 (t) REVERT: G 46 LYS cc_start: 0.8143 (pptt) cc_final: 0.7937 (pptt) outliers start: 19 outliers final: 3 residues processed: 164 average time/residue: 1.2873 time to fit residues: 223.5797 Evaluate side-chains 143 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 52 optimal weight: 0.0470 chunk 95 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 287 ASN A 188 HIS A 269 ASN A 306 GLN E 82 GLN G 24 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8888 Z= 0.147 Angle : 0.490 7.430 12047 Z= 0.256 Chirality : 0.041 0.164 1382 Planarity : 0.003 0.038 1518 Dihedral : 4.620 85.362 1209 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.58 % Allowed : 16.09 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 1097 helix: 2.33 (0.26), residues: 396 sheet: 0.35 (0.30), residues: 276 loop : 0.19 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS B 142 PHE 0.010 0.001 PHE B 199 TYR 0.011 0.001 TYR R 107 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 0.956 Fit side-chains REVERT: R 79 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8093 (mm) REVERT: R 288 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8479 (p) REVERT: A 29 LYS cc_start: 0.7801 (tttt) cc_final: 0.7408 (tmmt) REVERT: A 270 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8308 (mmmm) REVERT: A 333 GLN cc_start: 0.7662 (tp40) cc_final: 0.7185 (tp-100) REVERT: B 212 ASP cc_start: 0.7228 (t70) cc_final: 0.6865 (t0) REVERT: B 259 GLN cc_start: 0.8038 (pt0) cc_final: 0.7614 (pt0) REVERT: E 157 ILE cc_start: 0.8490 (mm) cc_final: 0.8231 (mp) REVERT: E 160 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.6601 (mtm110) REVERT: E 244 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7250 (tmtm) REVERT: G 21 MET cc_start: 0.6224 (tmm) cc_final: 0.5955 (tpt) outliers start: 24 outliers final: 6 residues processed: 154 average time/residue: 1.3297 time to fit residues: 216.7438 Evaluate side-chains 143 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain E residue 244 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0050 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 287 ASN A 269 ASN A 306 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8888 Z= 0.295 Angle : 0.562 8.160 12047 Z= 0.291 Chirality : 0.044 0.147 1382 Planarity : 0.004 0.038 1518 Dihedral : 4.908 84.470 1209 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.11 % Allowed : 17.06 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1097 helix: 2.23 (0.26), residues: 396 sheet: 0.23 (0.30), residues: 279 loop : 0.15 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS R 103 PHE 0.012 0.002 PHE R 112 TYR 0.019 0.001 TYR R 183 ARG 0.008 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: R 288 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8551 (p) REVERT: A 29 LYS cc_start: 0.7885 (tttt) cc_final: 0.7489 (tmmt) REVERT: A 242 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7522 (mtm180) REVERT: A 270 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8258 (mmmm) REVERT: A 333 GLN cc_start: 0.7684 (tp40) cc_final: 0.7205 (tp-100) REVERT: B 212 ASP cc_start: 0.7262 (t70) cc_final: 0.6829 (t70) REVERT: B 259 GLN cc_start: 0.8033 (pt0) cc_final: 0.7593 (pt0) REVERT: E 157 ILE cc_start: 0.8522 (mm) cc_final: 0.8161 (mp) REVERT: E 160 ARG cc_start: 0.7367 (mtm-85) cc_final: 0.6650 (mtm110) REVERT: E 244 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7255 (tmtm) REVERT: G 46 LYS cc_start: 0.8155 (pptt) cc_final: 0.7945 (pptt) outliers start: 29 outliers final: 13 residues processed: 152 average time/residue: 1.4154 time to fit residues: 226.9809 Evaluate side-chains 146 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 13 ASN Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 288 SER Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 244 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 0.1980 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 102 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 287 ASN A 22 ASN A 269 ASN A 306 GLN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8888 Z= 0.128 Angle : 0.486 7.329 12047 Z= 0.255 Chirality : 0.041 0.156 1382 Planarity : 0.003 0.035 1518 Dihedral : 4.605 86.802 1209 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.04 % Allowed : 18.24 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.26), residues: 1097 helix: 2.33 (0.26), residues: 397 sheet: 0.36 (0.30), residues: 273 loop : 0.15 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.009 0.001 PHE A 189 TYR 0.016 0.001 TYR R 183 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 0.778 Fit side-chains REVERT: A 29 LYS cc_start: 0.7784 (tttt) cc_final: 0.7399 (tmmt) REVERT: A 242 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7538 (mtm180) REVERT: A 270 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8234 (mmmm) REVERT: A 333 GLN cc_start: 0.7669 (tp40) cc_final: 0.7282 (tp-100) REVERT: B 212 ASP cc_start: 0.7158 (t70) cc_final: 0.6818 (t0) REVERT: B 259 GLN cc_start: 0.8014 (pt0) cc_final: 0.7618 (pt0) REVERT: B 262 MET cc_start: 0.8391 (ttm) cc_final: 0.7924 (ttm) REVERT: E 157 ILE cc_start: 0.8393 (mm) cc_final: 0.8148 (mp) REVERT: E 160 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.6572 (mtm110) REVERT: E 244 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7181 (tmtm) REVERT: G 21 MET cc_start: 0.6269 (tmm) cc_final: 0.5967 (tpt) outliers start: 19 outliers final: 6 residues processed: 144 average time/residue: 1.4156 time to fit residues: 215.1287 Evaluate side-chains 131 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 244 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 287 ASN A 22 ASN A 269 ASN A 306 GLN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8888 Z= 0.168 Angle : 0.500 7.005 12047 Z= 0.260 Chirality : 0.042 0.163 1382 Planarity : 0.004 0.039 1518 Dihedral : 4.583 84.844 1209 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.93 % Allowed : 18.13 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1097 helix: 2.38 (0.26), residues: 397 sheet: 0.27 (0.30), residues: 279 loop : 0.22 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE B 199 TYR 0.013 0.001 TYR R 183 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.991 Fit side-chains REVERT: A 29 LYS cc_start: 0.7802 (tttt) cc_final: 0.7426 (tmmt) REVERT: A 242 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7551 (mtm180) REVERT: A 270 LYS cc_start: 0.8525 (mmmm) cc_final: 0.8200 (mmmm) REVERT: A 333 GLN cc_start: 0.7693 (tp40) cc_final: 0.7305 (tp-100) REVERT: B 212 ASP cc_start: 0.7210 (t70) cc_final: 0.6795 (t0) REVERT: B 259 GLN cc_start: 0.7998 (pt0) cc_final: 0.7621 (pt0) REVERT: B 262 MET cc_start: 0.8454 (ttm) cc_final: 0.8125 (ttm) REVERT: E 157 ILE cc_start: 0.8374 (mm) cc_final: 0.8131 (mp) REVERT: E 160 ARG cc_start: 0.7279 (mtm-85) cc_final: 0.6548 (mtm110) REVERT: E 244 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7190 (tmtm) REVERT: G 21 MET cc_start: 0.6277 (tmm) cc_final: 0.5987 (tpt) outliers start: 18 outliers final: 10 residues processed: 141 average time/residue: 1.4245 time to fit residues: 211.8475 Evaluate side-chains 143 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 244 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 287 ASN A 22 ASN A 269 ASN A 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8888 Z= 0.162 Angle : 0.496 7.165 12047 Z= 0.259 Chirality : 0.041 0.175 1382 Planarity : 0.003 0.037 1518 Dihedral : 4.546 84.807 1209 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.93 % Allowed : 18.78 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 1097 helix: 2.38 (0.26), residues: 398 sheet: 0.36 (0.30), residues: 274 loop : 0.19 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 301 PHE 0.010 0.001 PHE B 199 TYR 0.013 0.001 TYR R 183 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.928 Fit side-chains REVERT: A 29 LYS cc_start: 0.7795 (tttt) cc_final: 0.7394 (tmmt) REVERT: A 251 ASP cc_start: 0.8507 (t70) cc_final: 0.8177 (t0) REVERT: A 270 LYS cc_start: 0.8515 (mmmm) cc_final: 0.8148 (mmmm) REVERT: A 306 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.7098 (mt0) REVERT: A 333 GLN cc_start: 0.7702 (tp40) cc_final: 0.7187 (tp-100) REVERT: B 212 ASP cc_start: 0.7170 (t70) cc_final: 0.6786 (t0) REVERT: B 217 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6325 (ptt) REVERT: B 259 GLN cc_start: 0.7997 (pt0) cc_final: 0.7527 (pt0) REVERT: B 262 MET cc_start: 0.8482 (ttm) cc_final: 0.8166 (ttm) REVERT: E 160 ARG cc_start: 0.7250 (mtm-85) cc_final: 0.6519 (mtm110) REVERT: E 244 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7212 (tmtm) REVERT: G 21 MET cc_start: 0.6265 (tmm) cc_final: 0.5873 (tpt) outliers start: 18 outliers final: 9 residues processed: 147 average time/residue: 1.4345 time to fit residues: 223.2208 Evaluate side-chains 147 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 244 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.0470 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 287 ASN A 22 ASN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8888 Z= 0.203 Angle : 0.519 7.287 12047 Z= 0.270 Chirality : 0.042 0.184 1382 Planarity : 0.004 0.037 1518 Dihedral : 4.606 84.105 1209 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.82 % Allowed : 19.31 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 1097 helix: 2.38 (0.26), residues: 397 sheet: 0.37 (0.30), residues: 274 loop : 0.19 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 301 PHE 0.010 0.001 PHE B 199 TYR 0.027 0.001 TYR R 183 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 0.925 Fit side-chains REVERT: A 29 LYS cc_start: 0.7815 (tttt) cc_final: 0.7403 (tmmt) REVERT: A 251 ASP cc_start: 0.8552 (t70) cc_final: 0.8187 (t0) REVERT: A 270 LYS cc_start: 0.8499 (mmmm) cc_final: 0.8130 (mmmm) REVERT: A 333 GLN cc_start: 0.7659 (tp40) cc_final: 0.7197 (tp-100) REVERT: A 337 ASP cc_start: 0.7835 (m-30) cc_final: 0.7566 (m-30) REVERT: B 212 ASP cc_start: 0.7192 (t70) cc_final: 0.6764 (t0) REVERT: B 259 GLN cc_start: 0.8000 (pt0) cc_final: 0.7521 (pt0) REVERT: E 160 ARG cc_start: 0.7278 (mtm-85) cc_final: 0.6565 (mtm110) REVERT: E 244 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7217 (tmtm) outliers start: 17 outliers final: 9 residues processed: 148 average time/residue: 1.4160 time to fit residues: 221.2712 Evaluate side-chains 146 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 244 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 269 ASN A 306 GLN E 39 GLN E 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8888 Z= 0.176 Angle : 0.519 7.673 12047 Z= 0.269 Chirality : 0.042 0.186 1382 Planarity : 0.003 0.038 1518 Dihedral : 4.599 84.065 1209 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.18 % Allowed : 20.28 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1097 helix: 2.42 (0.26), residues: 397 sheet: 0.34 (0.30), residues: 269 loop : 0.22 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 301 PHE 0.010 0.001 PHE B 199 TYR 0.028 0.001 TYR R 183 ARG 0.009 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7812 (tttt) cc_final: 0.7428 (tmmt) REVERT: A 242 ARG cc_start: 0.7782 (mtm180) cc_final: 0.7560 (mtm180) REVERT: A 251 ASP cc_start: 0.8546 (t70) cc_final: 0.8185 (t0) REVERT: A 270 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8132 (mmmm) REVERT: A 333 GLN cc_start: 0.7660 (tp40) cc_final: 0.7190 (tp-100) REVERT: A 337 ASP cc_start: 0.7822 (m-30) cc_final: 0.7551 (m-30) REVERT: B 212 ASP cc_start: 0.7205 (t70) cc_final: 0.6771 (t0) REVERT: B 217 MET cc_start: 0.6438 (ptt) cc_final: 0.6235 (ptt) REVERT: B 259 GLN cc_start: 0.7978 (pt0) cc_final: 0.7504 (pt0) REVERT: B 262 MET cc_start: 0.8253 (ttm) cc_final: 0.7862 (ttm) REVERT: E 93 MET cc_start: 0.8380 (ttp) cc_final: 0.7958 (ttm) REVERT: E 160 ARG cc_start: 0.7250 (mtm-85) cc_final: 0.6505 (mtm110) REVERT: E 244 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7252 (tmtm) outliers start: 11 outliers final: 9 residues processed: 143 average time/residue: 1.4327 time to fit residues: 216.2659 Evaluate side-chains 143 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 SER Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain E residue 244 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 269 ASN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.156989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.111137 restraints weight = 10895.136| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.40 r_work: 0.3308 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8888 Z= 0.246 Angle : 0.553 7.706 12047 Z= 0.286 Chirality : 0.043 0.183 1382 Planarity : 0.004 0.036 1518 Dihedral : 4.727 82.584 1209 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.61 % Allowed : 19.96 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 1097 helix: 2.39 (0.26), residues: 396 sheet: 0.31 (0.30), residues: 269 loop : 0.16 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 PHE 0.011 0.002 PHE B 199 TYR 0.026 0.001 TYR R 183 ARG 0.009 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4215.45 seconds wall clock time: 74 minutes 4.54 seconds (4444.54 seconds total)